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

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Basic information

Entry
Database: PDB / ID: 9qdg
TitleNitratidesulfovibrio vulgaris [FeFe] hydrogenase crystallized in the sodium propionate buffer at pH 5.0
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: 1.02 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

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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
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-105 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.724, 87.705, 89.684
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-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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 1.79 Å3/Da / Density % sol: 31.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium propionate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.688805 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: 0.688805 Å / Relative weight: 1
ReflectionResolution: 1.02→44.84 Å / Num. obs: 198603 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.077 / Rrim(I) all: 0.205 / Χ2: 1.03 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
5.59-44.8412.50.05832.313830.9990.0230.0630.81
1.02-1.0411.64.2890.696480.2881.8964.7021.01

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→44.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2071 9942 5.009 %
Rwork0.1935 188556 -
all0.194 --
obs-198498 99.682 %
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: 13.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å20 Å2
2---0.781 Å20 Å2
3---0.541 Å2
Refinement stepCycle: LAST / Resolution: 1.02→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 41 421 4169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.0470.3716930.34913766X-RAY DIFFRACTION99.1497
1.047-1.0750.3217110.3213472X-RAY DIFFRACTION99.8873
1.075-1.1060.2927060.29713145X-RAY DIFFRACTION99.8558
1.106-1.140.2736340.27812744X-RAY DIFFRACTION99.7986
1.14-1.1780.2726600.25912348X-RAY DIFFRACTION99.7087
1.178-1.2190.2596660.24311948X-RAY DIFFRACTION99.6603
1.219-1.2650.2366400.23911475X-RAY DIFFRACTION99.4663
1.265-1.3170.2396800.22510982X-RAY DIFFRACTION99.4118
1.317-1.3750.2325670.21510709X-RAY DIFFRACTION99.8406
1.375-1.4420.2115200.20410241X-RAY DIFFRACTION99.4915
1.442-1.520.1884600.1819792X-RAY DIFFRACTION100
1.52-1.6120.1764830.179274X-RAY DIFFRACTION100
1.612-1.7230.1794340.1658740X-RAY DIFFRACTION100
1.723-1.8610.1764250.1648137X-RAY DIFFRACTION100
1.861-2.0390.1833940.167470X-RAY DIFFRACTION99.8603
2.039-2.2790.1713500.1616804X-RAY DIFFRACTION99.4993
2.279-2.630.22830.1635978X-RAY DIFFRACTION98.2888
2.63-3.2180.1942810.185128X-RAY DIFFRACTION99.963
3.218-4.540.1732090.1594062X-RAY DIFFRACTION100
4.54-44.840.1821460.1672342X-RAY DIFFRACTION100

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