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

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Basic information

Entry
Database: PDB / ID: 9qdd
TitleNitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3
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: 1.201 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
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-106 kcal/mol
Surface area17410 Å2
Unit cell
Length a, b, c (Å)49.713, 87.77, 89.798
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.: 445 / 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: 1.8 Å3/Da / Density % sol: 31.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate pH 5.3

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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: 1.19→44.939 Å / Num. obs: 114591 / % possible obs: 90.9 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.095 / Rrim(I) all: 0.251 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.52-44.912.50.0628980.9980.0240.067
1.19-1.218.34.60830950.3052.4315.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.201→44.939 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.051 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2202 5661 5.147 %
Rwork0.2003 104316 -
all0.201 --
obs-109977 89.418 %
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: 15.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.168 Å2-0 Å2-0 Å2
2---1.19 Å20 Å2
3---1.021 Å2
Refinement stepCycle: LAST / Resolution: 1.201→44.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 41 445 4193
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
1.201-1.2321.8781291.85820451.8690090.5070.47124.13141.853
1.232-1.2660.9583241.01155401.00887710.6250.6466.85670.983
1.266-1.3030.5693540.53470190.53585160.830.84886.57820.516
1.303-1.3430.3614250.35875370.35882980.9180.92595.95080.364
1.343-1.3870.3113600.30873960.30880360.9370.9496.51570.326
1.387-1.4350.2693490.25571640.25677650.940.95196.75470.266
1.435-1.4890.2673680.23169780.23375610.9490.9697.15650.236
1.489-1.550.2393380.22266750.22372420.9610.96696.83790.223
1.55-1.6190.2443690.20764000.20969310.960.97397.66270.205
1.619-1.6980.2253510.19961890.266690.9660.97598.06570.196
1.698-1.7890.2022810.19559540.19663460.9740.97898.25090.192
1.789-1.8980.2173150.18356240.18560150.9760.98198.73650.178
1.898-2.0290.2063060.1852980.18156660.9750.98298.90580.175
2.029-2.1910.1892920.16848900.16953030.9790.98497.71830.163
2.191-2.3990.2072590.15645780.15848700.9750.98599.32240.153
2.399-2.6820.1762070.15542050.15644320.9810.98599.54870.154
2.682-3.0950.1852330.16837080.16939490.9780.98299.79740.169
3.095-3.7860.1751900.15431680.15533630.9820.98699.85130.16
3.786-5.3350.1591420.15224510.15226540.9890.9997.70160.161
5.335-44.9390.181690.19214970.19215690.9850.98499.80880.202

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