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- PDB-9r9v: [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hilden... -

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Basic information

Entry
Database: PDB / ID: 9r9v
Title[FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 7.00
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / holo 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 / 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 ...Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 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 / 4Fe-4S dicluster 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 / DI(HYDROXYETHYL)ETHER / 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: 1.25 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
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 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)54,8608
Polymers53,1062
Non-polymers1,7546
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.365, 87.269, 88.887
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Periplasmic [Fe] hydrogenase ... , 2 types, 2 molecules BA

#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) / References: UniProt: P07603, ferredoxin hydrogenase
#2: Protein Periplasmic [Fe] hydrogenase large subunit / Fe hydrogenlyase


Mass: 43023.570 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

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Non-polymers , 5 types, 389 molecules

#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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% (w/v) PEG 4000, 1 M LiCl, 0.1 M sodium acetate, 16.5 mM citric acid, 24.75 mM HEPES, 33 mM CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0333 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 9, 2023
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.25→44.44 Å / Num. obs: 106649 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Rrim(I) all: 0.126 / Χ2: 0.98 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
6.85-44.4411.20.08933.47660.9930.0360.0961.699.8
1.25-1.278.10.8983.951070.7760.4931.0030.8997.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→44.44 Å / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.035 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1532 5474 5.137 %
Rwork0.1346 --
obs-106565 99.815 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.635 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.495 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 63 383 4159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.214150.1917213X-RAY DIFFRACTION97.8827
1.282-1.3180.1943670.1687237X-RAY DIFFRACTION99.9343
1.318-1.3560.1893640.1557066X-RAY DIFFRACTION99.9865
1.356-1.3970.1573440.1446839X-RAY DIFFRACTION100
1.397-1.4430.163430.1346625X-RAY DIFFRACTION100
1.443-1.4940.1523190.1266455X-RAY DIFFRACTION99.9705
1.494-1.550.163400.1216147X-RAY DIFFRACTION99.8768
1.55-1.6130.1283320.115967X-RAY DIFFRACTION99.9683
1.613-1.6850.1472670.1165776X-RAY DIFFRACTION100
1.685-1.7670.1443520.1165434X-RAY DIFFRACTION100
1.767-1.8620.1392440.1155254X-RAY DIFFRACTION99.9818
1.862-1.9750.142780.1224985X-RAY DIFFRACTION99.943
1.975-2.1110.1382800.1224603X-RAY DIFFRACTION99.9182
2.111-2.280.1322620.124330X-RAY DIFFRACTION100
2.28-2.4970.1422260.1274019X-RAY DIFFRACTION100
2.497-2.7910.1781790.1463681X-RAY DIFFRACTION100
2.791-3.220.1792110.1493204X-RAY DIFFRACTION99.9707
3.22-3.9390.1421750.1382746X-RAY DIFFRACTION99.8633
3.939-5.5480.1411070.1362213X-RAY DIFFRACTION100
5.548-44.440.172690.1811298X-RAY DIFFRACTION99.9269

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