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- PDB-9qdc: Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in ... -

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Basic information

Entry
Database: PDB / ID: 9qdc
TitleNitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6
Components
  • Periplasmic [Fe] hydrogenase large subunit
  • Periplasmic [Fe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / iron-sulfur cluster / metalloenzyme / hydrogen production
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase ...Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-402 / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsBikbaev, K. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1476/4-1 Germany
CitationJournal: To Be Published
Title: Impact of the acidic conditions on [FeFe]-Hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough
Authors: Bikbaev, K. / Span, I.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Periplasmic [Fe] hydrogenase small subunit
A: Periplasmic [Fe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8896
Polymers54,4802
Non-polymers1,4104
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-105 kcal/mol
Surface area17380 Å2
Unit cell
Length a, b, c (Å)49.535, 87.568, 89.2
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic [Fe] hydrogenase small subunit / Fe hydrogenlyase small chain


Mass: 10082.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hydB, DVU_1770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): (delta)iscR / References: UniProt: P07603, ferredoxin hydrogenase
#2: Protein Periplasmic [Fe] hydrogenase large subunit / Fe hydrogenlyase


Mass: 44397.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hydA, DVU_1769 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): (delta)iscR / References: UniProt: P07598, ferredoxin hydrogenase
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 35% (w/v) PEG 4000, 1M LiCl, 0.1M sodium formate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 24, 2023
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.49→49.53 Å / Num. obs: 63886 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.068 / Rrim(I) all: 0.181 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.16-49.5311.60.0694720.9960.0280.075
1.49-1.5212.71.23330950.7940.5161.338

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.491→44.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.059 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1815 3203 5.019 %
Rwork0.1473 60615 -
all0.149 --
obs-63818 99.636 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å2-0 Å2-0 Å2
2---0.958 Å20 Å2
3---0.941 Å2
Refinement stepCycle: LAST / Resolution: 1.491→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 41 410 4158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.491-1.5290.2462470.20943690.21146670.9570.96798.90720.2
1.529-1.5710.222640.19342640.19545540.9660.97299.42910.182
1.571-1.6170.192290.16941790.1744170.9750.9899.79620.158
1.617-1.6660.21940.16141190.16343280.9720.98299.65340.148
1.666-1.7210.2222000.15539830.15841890.9680.98499.85680.142
1.721-1.7810.1881960.1538320.15140310.9780.98599.92560.135
1.781-1.8480.1812330.13936620.14238980.980.98799.9230.125
1.848-1.9240.1641890.13235930.13437890.9820.98999.81530.12
1.924-2.0090.1772060.13433970.13736040.9810.98899.97230.124
2.009-2.1070.1451420.13232940.13234670.9860.98999.10590.121
2.107-2.2210.2021890.13431000.13833050.9760.98999.51590.126
2.221-2.3550.1691440.13229960.13431480.9830.98999.74590.126
2.355-2.5170.1921230.14128170.14329420.9770.98799.9320.135
2.517-2.7180.2011330.14626260.14927650.9770.98799.7830.142
2.718-2.9760.161350.15624150.15625500.9830.9851000.155
2.976-3.3260.198860.16222320.16323190.9780.98599.95690.165
3.326-3.8370.1631120.14719350.14820610.9860.98899.32070.156
3.837-4.690.138910.12116470.12217700.9890.99298.19210.135
4.69-6.5970.185550.15113430.15213980.9820.9891000.168
6.597-44.640.208350.1578120.1598480.9790.98599.88210.18

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