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- PDB-9qd6: High resolution structure of the artificially maturated [FeFe]-hy... -

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Basic information

Entry
Database: PDB / ID: 9qd6
TitleHigh resolution structure of the artificially maturated [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough
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 / electron transfer activity / periplasmic space / 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: 1.18 Å
AuthorsBikbaev, K. / Harand, T. / Scheuenstuhl, L. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1476/4-1 Germany
CitationJournal: Chem Sci / Year: 2026
Title: Subunit fusion unlocks rapid in vitro maturation for slowly activating heterodimeric [FeFe]-hydrogenases
Authors: Winkler, M.H. / Jaenecke, J. / Bikbaev, K. / Bronold, J. / Yadav, S. / Apfel, U.P. / Birrell, J.A. / Span, I. / Plumere, N. / Leger, C. / Malagnini, M.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 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)56,2478
Polymers54,4802
Non-polymers1,7676
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.444, 87.273, 89.169
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) / 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

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Non-polymers , 5 types, 381 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 1.77 Å3/Da / Density % sol: 30.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.688793 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: 0.688793 Å / Relative weight: 1
ReflectionResolution: 1.18→49.44 Å / Num. obs: 127101 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.071 / Rrim(I) all: 0.19 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.46-49.4411.70.0539090.9990.0210.057
1.18-1.213.91.70362100.6670.6851.837

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→44.624 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.034 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1685 6464 5.089 %
Rwork0.1513 120544 -
all0.152 --
obs-127008 99.859 %
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: 12.264 Å2
Baniso -1Baniso -2Baniso -3
1-0.123 Å2-0 Å2-0 Å2
2--0.081 Å2-0 Å2
3----0.203 Å2
Refinement stepCycle: LAST / Resolution: 1.18→44.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 65 375 4166
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
1.18-1.2110.2344440.22788670.22893220.9630.96499.8820.222
1.211-1.2440.2294920.21785430.21790350.9640.9671000.21
1.244-1.280.2254130.20983790.2187960.9660.9799.95450.199
1.28-1.3190.2184540.19681310.19786010.9670.97499.8140.185
1.319-1.3620.2043820.18778900.18883030.9720.97699.62660.174
1.362-1.410.1953950.17676240.17780750.9750.97999.30650.161
1.41-1.4630.1843820.16173900.16277860.9760.98399.82020.145
1.463-1.5230.1573490.1471300.1474790.9840.9881000.126
1.523-1.5910.1413970.12868340.12972310.9880.991000.115
1.591-1.6680.1413660.11965050.12168740.9880.99199.95640.107
1.668-1.7580.1473070.1262690.12165760.9860.9911000.109
1.758-1.8650.1423120.12358880.12462000.9880.9911000.113
1.865-1.9930.1553190.12755400.12858590.9870.9911000.12
1.993-2.1530.1623050.13451870.13554970.9840.98999.9090.13
2.153-2.3580.1672790.12947790.13150620.9850.9999.9210.128
2.358-2.6350.1712100.14543370.14645760.9840.98899.36630.147
2.635-3.0410.1742450.15838230.15940680.9810.9851000.165
3.041-3.720.1611940.15632910.15634850.9840.9871000.169
3.72-5.2430.1391460.14525880.14427350.990.9999.96340.165
5.243-44.6240.183730.16615490.16716260.9830.98499.7540.187

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