Using a micro-seeding method, protein crystals of the rectangular shape appeared after two days, and continued to grow to a terminal size 0.5 × 0.4 × 0.4 mm³ within one week in an incubator at 18 °C (Figure 1). These crystals were sensitive to a variation of precipitant concentration while being transferred to the cryo-protectent solution containing glycerol (20%). Several crystals were tested before data collection because of a mosaicity > 1° that caused an overlap of diffraction spots in the high-resolution regions. Radiation damage was observed on protracted exposure during data collection, which caused I/σ(I) to decrease and R_sym to increase. Assuming the presence of two Fld molecules per asymmetric unit, the Matthew’s coefficient is estimated to be 2.06 ų Da⁻¹, corresponding to a solvent content of 40.4% [31], which is within the normal range for protein crystals. A calculation of the self-rotation function showed extra peaks in addition to the crystallographic orthorhombic symmetry in κ = 180°, indicating that the non-crystallographic two-fold axes exist in the local symmetry of Fld molecules, which confirms the dimeric structure of Fld. Details of data statistics are summarized in Table 1.

Although the crystal of Fld diffracted to resolution ~1.2 Å with completeness 99.7%, the data in the resolution shell 1.2–1.3 Å with a high R_sym (~70%) was unusable in the structural refinement; we therefore performed the refinement in a resolution range 30–1.3 Å. The refined structural model of Fld at resolution 1.3 Å gave factors R_work = 18% and R_free = 21%. According to Ramachandran plot, the stereochemistry showed that 282 amino acids are in the most favored region and four residues in the allowed region, indicating a satisfactory structural refinement of dimeric Fld.

The overall structure of the monomer Fld, consistent of 145 amino acids (2–146), comprises five β-helices and five β-sheets in order ββββββββββ folding into a sandwich conformation equipping five β-sheets in the middle with two and three β-helices surrounding on both sides (Figure 2a). The co-factor FMN is clearly visible with the electron density, and is located near the protein surface. The framework of hydrogen bonds involving main-chain atoms, side-chain atoms and various water molecules, contributes greatly to the stability of FMN. The dimensions of dimeric Fld are ~59 × 39 × 35 ų, with a surface area 3644 Ų accessible to solvents. An inspection of the electrostatic surface shows that the negative charges distribute almost all around the protein surface because Fld has a small pI value (~4.08). The amino-acid composition of Fld contains large proportions of Asp (8.9%) and Glu (10.3%), which contribute the major negative charges on the protein surface. Some residues with polar side chains, such as Ser (5.5%) and Thr (6.8%), also provide negative charges on the surface. The Fld dimer forms a long and connected, negatively charged, surface with Asp40, Asp62, Asp63, Glu64, Glu66, Gln68, Glu69, Asp70, Tyr75, Glu76, Asp77, Thr99 and Tyr100, and with FMN located at both sides (Figure 2b).

In the high resolution Fld structure (1.3 Å), the position of FMN was well defined by the electron density, resolving a hole of the aromatic ring (Figure 3). The Fld exposes its co-factor FMN to the surface with an accessible surface area ~32.5 Ų. The structure of FMN comprises two major parts; the “head” part with the isoalloxazine ring is more hydrophobic, whereas the “tail” part with the phosphate group is more hydrophilic. The electrostatic surface of the FMN-binding pocket reveals that the binding site for FMN is hydrophobic with aromatic residues, e.g., Trp60 and Phe101, whereas the binding pocket for the phosphate group is positively charged (Figure 3a). Four major loops, including Ser10–Thr15, Asp95–Gly103, Thr59–Asp63 and Asp127–Asp131, contribute to the formation of the FMN binding pocket (~20 × 9 × 9 ų). Various interactions involved in the fixation of the co-factor FMN in the binding site are summarized in Table 2. The isoalloxazine ring of FMN was stabilized with loops Asp95–Gly103 and Thr59–Asp63, in which Trp60 and Tyr98 located at both sides of the isoalloxazine ring are the most important for providing direct π-π interactions (Figure 3b). The distances from Trp60 and Tyr98 to FMN are 3.9 and 3.7 Å, respectively. The amino acids from Ser10 to Thr15 form a loop that provides several hydrogen bonds to stabilize the phosphate group of FMN.

An overall structural flexibility of dimeric Fld was examined with temperature B-factors of the residues (Figure 4a). The most dynamic region is the loop Thr59–Asp63 with an average B-value ~37 Ų in the monomer A (Figure 4b). The loop Ser96–Thr99 in the monomer B also has a large overall B-value (~20 Ų). These two dynamic loops are, notably, utilized to coordinate with the co-factor FMN. Moreover, the C-terminal β-helices (Ser132–Arg145) in both monomers also have large B-values (~22 Ų). The individual residues Glu32 (~27 Ų) and Gly49 (~20 Ų) in the monomer A show large temperature factors for their dynamic character.

Superimposing the structures of the two monomers in the Fld dimer reveals a small r.m.s. deviation (0.37 Å), implying that the overall folding of each of the monomers is similar (Figure 4c,d), but a detailed inspection of the conformation shows that the structures and positions of some main chains and the co-factors are notably altered, especially a conformational alteration around the active site. This comparison showed that two FMN-coordination loops (Thr59–Asp63 and Ser96–Thr99) are not at the same corresponding position in the two monomers, in which Asp63 and Tyr98 exhibit the largest vibration distances ~6.2 and 1.5 Å, respectively. The position of FMN also exhibits a great deviation, up to 1.0 Å. Moreover, the conformations of residues on the protein surface, such as Glu20, Asp40 and Glu129, are altered.

The structures of the Flds in varied oxidation states were solved in various species, such as Megasphaera elsdenii[32], Clostridium beiherinckii MP [33], Anacystis nidulans[14] and Desulfovibrio vulgaris[27]. All structural results indicate that the Flds prefer the reduction from the oxidized state to the semiquinone state, which is accomplished by a peptide flip at the glycine residue (Gly61 in D. gigas) and with formation of a hydrogen bond between atom N5 of FMN and the carbonyl oxygen of the glycine main chain (Figure 4d). A similar state was evaluated in the Fld from D. gigas, which has the same structural characteristic as a semiquinone state. The peptide of Gly61 points to atom N5 of FMN with distances 3.7 and 3.6 Å, respectively, in monomers A and B. However, the structure and character of FMN are easily affected by X-ray radiation damage [34,35]. Therefore, we could not exclude the possibility that the peptide flipping of Gly61 is raised by the radiation damage.

Several residues of Fld from D. vulgaris were investigated by mutations for their roles in modulated redox potentials [29,30]. Superimposed structures of two monomers from the D. gigas Fld dimer reveal that those corresponding residues are deviated with different orientations, implying that a similar modulation of the redox potential might exist in D. gigas Fld. The side-chain conformations of the conserved residues Gly61 and Asp95 among various Flds from Desulfovibrio sp. are altered about 1.0 and 0.7 Å, respectively (Figure S1). In addition, the mutation S64C on the non-conserved residue Ser64 in Fld from D. vulgaris might play a role in the redox potential [36]. In D. gigas Fld, the corresponding residues Glu64 point their side chains in opposite directions with a deviated distance 5.4 Å, observed in the two superimposed monomer structures.

The self-rotation function confirms the presence of two-fold axes for the non-crystallographic symmetry, which generates the dimer structure of Fld. If the position of FMN in the Fld is defined as the “head” of the structure, the dimer model is packed in an orientation head to head. The molecular packing in the unit cell shows that there are four dimer structures present in space group P2₁2₁2₁ in the crystals (Figure 5b). Gel filtration during protein purification showed that Fld exists as a dimer in solution (Figure S2), which corresponds to the crystal state, implying that the dimeric structure head to head might be the functional unit.

The contact area in the dimeric interface is ~770 Ų (Figure 5a). There are 35 major hydrogen bonds with distances less than 3.5 Å to contribute to this contact area. The residues with interaction distances stabilizing the dimer structure are listed in Table 3. Briefly, two segments are mainly involved in dimerization; one is the dynamic loop Thr59–Asp63 mentioned previously, and the other is the β-helix Gly103–Leu155. The interface of dimerization notably contains no charge or slight positive charge distribution; dimerization hence exposes and creates a more negatively charged environment on the surface of the Fld dimer by concealing the uncharged or positively charged residues at the dimeric interface.

Flds are reported to be multiple functional enzymes, which could interact with various partners, in various reactions [2–12], but the structures of Fld in a complex with its partners are seldom investigated. How the Fld utilizes its key residues to recognize and interact with partner proteins is unclear. Some authors proposed that the displacements of the Trp60-containing loop might be an initial point for the protein-partner recognition [28]. The same loop for the partner recognition was proposed in Fld from E. coli[37].

Our Fld structure is a dimer, as in the native state, which allows us to probe the binding site for its partners. From the view of the active site, FMN is the center of the electron transfer in Fld. An inspection of the co-factor environment shows that dimerization could bring two FMN close to each other with a short distance 17 Å. Within the range between two FMN, a large negatively charged region is formed (Figure 2b), which is suitable for the interaction with its protein partner containing the positively charged surface. In addition, two dynamic loops, which might be involved in the protein function mentioned previously, and two FMN from the dimer are positioned in a line with order Thr59–Asp63/A, FMN/A, Asp95–Tyr100/A, Asp95–Tyr100/B, FMN/B and Thr59–Asp63/B (Figure 2b). The loop Thr59–Asp63 is the corresponding loop of the Trp60-contaning loop that was investigated previously [28,37]. The crystal structure of Fld from D. gigas might thus explain that the dimeric form is the functional unit due to the aligned negatively charged region formed by dimerization, in which two flexible loops might serve for the protein-partner recognition. Moreover, through dimerization, the isoalloxazine rings of FMN move nearer each other, which could presumably facilitate the transfer of electrons from the electron donor to the acceptor. The dimerization hence likely enables Fld to receive or to donate electrons efficiently from or to the protein partner.

The structure of Fld from D. gigas was compared with the structures from D. vulgaris (PDB: 5FX2) and D. desulfuricans (PDB: 3KAQ) of a semiquinone state. Superimposed structures of Flds from D. gigas with D. vulgaris and D. desulfuricans reveal a similar folding with the r.m.s.d ~0.55 Å and 0.75 Å, respectively, for all atoms. The major structural differences arise at two dynamic loops Thr59–Asp63 and Asp95–Tyr100, which interact with FMN, and the loop Asp127–Asp131 that contributes to the formation of a FMN-binding pocket. An analysis of the hydrogen bonds between the FMN and residues of Flds from various species shows that the interactions (43) within distance 3.5 Å in D. gigas are fewer than those in D. vulgaris (51) and D. desulfuricans (50), indicating that the binding force of FMN at the active site is weaker in D. gigas Fld. The interaction distances between atom N5 of FMN and the carbonyl oxygen of Gly61 in the Fld dimer of D. gigas (3.6–3.7 Å) are notably greater than that of D. vulgaris (3.1 Å) and D. desulfuricans (2.8 Å).

D. gigas (ATCC 19364) was anaerobically grown as described previously [38]. All purification steps of Fld were modified from the previous report [39] and performed at 4 °C in a cool room. The cells were suspended in Tris buffer (20 mM, pH 7.6) at concentration about 0.5 g of cells per 1 mL of buffer, subsequently subjected to cell disruption with ultra-sonication and directed through a high-pressure homogenizer (20,000 psi, 2 cycles, EmulsiFlex-C3, Avetin Inc., Ottawa, Canada). The lysed mixture was first centrifuged (12,100× g) for 20 min to remove larger particles; the supernatant was collected and ultra-centrifuged (194,000× g) for 2 h to remove the membrane fractions. To maintain the sample in the same condition, the supernatant was dialyzed against Tris buffer (20 mM, pH 7.6) over night in a cool room using a dialysis tube (5 kDa M.W. cut-off, purchased form Spectra). The sample was then directly loaded into the first DE-52 column, which was pre-equilibrated with the initial buffer (Tris, 20 mM, pH 7.6). The gradients of Tris (pH 7.6) from 20 mM to 0.5 M served to separate several fractions. The peak eluted around 0.35 M Tris with a yellow color containing Fld was collected and loaded into the second “hydroxyaptite” (HTP) column. After the sample was loaded on the column, the gradient of Tris was decreased from 0.35 M to 0 M; the buffer was then replaced with phosphate (pH 7.6) with gradient increasing from 0 M to 0.4 M. The fractions of the yellow color were collected again and concentrated to load into the third column–Sephadex G50, in which the Fld was purified and desalted. At this stage, SDS-page showed that the Fld factions were still contaminated with other proteins at small fractions. Further purification with the ion-exchange column was thus applied to remove the minor contaminations. The sample was loaded onto the final column—the DEAE Bio-gel, and eluted with a linear gradient of Tris buffer (pH 7.6) from 0.25 M to 0.5 M. The yield of the protein was approximately 0.2 mg per gram of D. gigas cells; the pure protein was analyzed with UV-visible spectra and SDS-PAGE (12%) with Coomassie Brilliant Blue staining.

Before crystallization trials, the protein sample was centrifuged to a concentration 8 mg/mL in Tris buffer (20 mM, pH 7.6). The crystal was screened in 96-well VDX^™ plates with the crystallization robot (Thermo Scientific Matrix Hydra II eDrop) according to the sitting-drop vapor-diffusion method at 18 °C. The crystallization plates were stored and monitored (Rocker Imager 54 (Formulatrix). Small crystals were observed from a condition containing PEG550 (30%, v/v), calcium chloride dihydrate (50 mM) and bis-Tris buffer (100 mM, pH 6.5) within six days after the initial screening using the Index kit (Hampton Research Co., Aliso Viejo, CA, USA). This condition was further refined to produce Fld crystals a little larger on varying the pH of the buffers and concentrations of PEG550 and CaCl₂; the improvement of the crystal quality was, however, inadequate for satisfactorily X-ray diffraction. To obtain crystals of superior quality, we performed the micro-seeding technique. The small crystals (0.1 × 0.1 × 0.1 mm) were first crushed into microcrystals with a thin glass wand in the Eppendorf (500 μL) containing the mother liquid solution, and transferred to fresh mother liquid for washing and dilution, several times. Only a few microcrystals were finally transferred to the hanging drops (2 μL) containing protein solution (1 μL) and reservoir solution (1 μL) in equal volumes, against the bottom reservoir solution (500 μL) containing PEG550 (25%, v/v), calcium chloride dihydrate (50 mM) and bis–Tris buffer (100 mM, pH 6.5) in the 24-well plate. Single crystals were observable two days after the micro-seeding technique and hang-drop vapor-diffusion method. Improved crystals of quality satisfactory for X-ray diffraction were used for data collection. The details of the data statistics are given in Table 1.

The protein crystals were initially screened and characterized using synchrotron radiation as a source of X-ray at SPXF beamline BL13B1 equipped with a CCD detector (Q315, ADSC, Poway, CA, USA) at National Synchrotron Radiation Research Center (NSRRC, Taiwan). Data collection was completed at Taiwan-contracted protein crystallographic beamline BL12B2 equipped with a CCD detector (Quantum-4R, ADSC, Poway, CA, USA) at SPring-8 in Japan. The crystal was transferred from a crystallization drop into a cryo-protectant solution (10 μL) containing PEG550 (25%, v/v), calcium chloride dihydrate (50 mM), glycerol (20%, v/v), and bis-Tris buffer (100 mM, pH 6.5) for a few seconds and mounted on a synthetic nylon loop (0.4–0.5 mm, Hampton Research Co., Aliso Viejo, CA, USA), and then flash-cooled in liquid nitrogen. For complete data collection, 180° rotations with 1.0° oscillation were measured with X-ray wavelength of 1.00 Å, exposure duration 15 s and distance 150 mm from the crystal to the detector, at 110 K in a dinitrogen stream using a cryo-system (X-Stream, Rigaku/MSC, Inc., Tokyo, Japan). All data were indexed, integrated and scaled using programs HKL2000[40].

The crystal structure of Fld was solved by molecular replacement using the structure of Fld from D. vulgaris (57.4% sequence identity; PDB code 1FX1 [27]) (Figure S1) as a search model. A molecular replacement solution was obtained with a correlation coefficient of 0.406 (the next highest solution had correlation coefficient 0.230) in the resolution range 20–4.0 Å using CNS v.1.2 [41], which confirmed the presence of two protein molecules per asymmetric unit. A randomly selected 5% of total observed reflections served as a test set for the free R-factor calculation. The model was rebuilt and adjusted according to the electron density with program Coot[42]. After rigid-body refinement using CNS v.1.2[39] in the resolution range 30–3 Å, factors R = 45.9% and R_free = 47.9% were obtained. After several cycles of manual adjustment and refinement, multiple conformations of various amino-acid residues, the model was refined with REFMAC5[43], which generated an R factor about 25%. The water molecules were added with water_pick in CNS v.1.2[44], which generated about 380 water molecules. After inspections of the electron density, 34 water molecules were deleted because of the low electron density level, generating the final model with factors R = 18% and R_free = 21%. The final structure was evaluated with RAMPAGE[45] and PROCHECK[43]. All figures of structures and electron densities were generated with PyMOL (http://www.rcsb.org) [46]. Coordinate and structure factor of Fld from D. gigas have been deposited with PDB under the accession code 4HEQ.