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- PDB-9r9t: [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hilden... -

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Basic information

Entry
Database: PDB / ID: 9r9t
Title[FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.81
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 / 2-(2-ETHOXYETHOXY)ETHANOL / 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: 2.076 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
A: Periplasmic [Fe] hydrogenase large subunit
B: Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2628
Polymers54,4802
Non-polymers1,7826
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.353, 87.132, 88.734
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 AB

#1: 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
#2: 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

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Non-polymers , 5 types, 64 molecules

#3: 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
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.81
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: 2.076→44.406 Å / Num. obs: 23704 / % possible obs: 99.6 % / Redundancy: 11.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.135 / Rrim(I) all: 0.332 / Χ2: 0.99 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
9.05-44.378.80.08620.83440.9960.0380.0951.15
2.08-2.139.91.4972.717230.6470.7221.6680.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.076→44.406 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 0.004 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.163 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2418 1182 4.998 %
Rwork0.1876 22468 -
all0.19 --
obs-23650 99.478 %
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: 28.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.387 Å2-0 Å2-0 Å2
2--2.421 Å2-0 Å2
3----2.034 Å2
Refinement stepCycle: LAST / Resolution: 2.076→44.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 65 58 3850
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
2.076-2.130.262790.22515620.22717180.9490.96395.5180.217
2.13-2.1890.269950.20915740.21216720.950.96999.82060.198
2.189-2.2520.267630.18915770.19316420.9650.97499.87820.179
2.252-2.3210.245610.19315130.19515760.9630.97499.87310.183
2.321-2.3970.241820.17514810.17815630.960.981000.165
2.397-2.4810.229740.16514330.16815070.9650.9821000.156
2.481-2.5740.224730.17513620.17814350.9670.9791000.163
2.574-2.6790.278860.18313030.18913890.9510.9771000.172
2.679-2.7970.271500.17912890.18313390.9480.981000.169
2.797-2.9330.263650.18812220.19112880.9570.97599.92240.177
2.933-3.0910.256660.19911600.20212280.9550.97399.83710.191
3.091-3.2780.236600.18211010.18511610.9580.9781000.176
3.278-3.5030.186390.17310640.17411030.970.981000.171
3.503-3.7810.213510.1659790.16710330.9740.98499.70960.166
3.781-4.1390.233410.188740.1839430.970.9897.03080.186
4.139-4.6230.219520.1788160.188680.970.981000.187
4.623-5.3280.246550.1627170.1677720.9710.9831000.173
5.328-6.5030.212370.26250.2016620.9730.9751000.213
6.503-9.0990.273270.215100.2135370.9470.9781000.222
9.099-44.4060.269260.2773060.2763370.9820.97598.51630.296

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