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- PDB-8rtg: Desulfovibrio desulfuricans [FeFe] hydrogenase in apo form -

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Basic information

Entry
Database: PDB / ID: 8rtg
TitleDesulfovibrio desulfuricans [FeFe] hydrogenase in apo form
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / apo 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
IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 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: Structure of [FeFe] hydrogenase in the holo and apo forms at room temperature
Authors: Bikbaev, K. / Martini, M.A. / Oberthuer, D. / Birrell, J.A. / Span, I.
History
DepositionJan 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: 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)55,5937
Polymers54,4802
Non-polymers1,1135
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.15, 84.786, 88.036
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.) Desulfovibrio desulfuricans (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.) Desulfovibrio desulfuricans (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 , 4 types, 334 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 7.6
Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 27.5 % Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.689 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 25, 2023
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.689 Å / Relative weight: 1
ReflectionResolution: 1.46→49.15 Å / Num. obs: 64587 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.179 / Rrim(I) all: 0.485 / Χ2: 1.01 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible allR split
8-49.15110.07421.74810.9980.030.0790.799.8
1.46-1.4914.43.55631340.5051.3933.820.9899.71.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.461→44.057 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.16 / SU B: 0.002 / SU ML: 0 / Average fsc free: 0.961 / Average fsc work: 0.9632 / Cross valid method: NONE / ESU R: 0.063 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1886 3166 4.908 %
Rwork0.1654 61340 -
all0.167 --
obs-64506 99.912 %
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: 15.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.604 Å20 Å20 Å2
2---0.204 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.461→44.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 26 329 4119
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
1.461-1.4980.6432200.63444480.63546860.7870.77299.61590.628
1.498-1.5390.3322190.3743890.36846080.9480.9351000.369
1.539-1.5840.2762010.25142630.25244640.9550.9591000.258
1.584-1.6330.2342380.20441220.20643600.9610.971000.209
1.633-1.6860.2322340.19539490.19741830.9640.9741000.198
1.686-1.7450.1962030.17238660.17340710.9730.9899.95090.172
1.745-1.8110.181790.16137760.16239550.9790.9831000.157
1.811-1.8850.1931730.15336420.15438180.9770.98699.92140.148
1.885-1.9680.1881720.15234740.15436470.9810.98699.97260.146
1.968-2.0640.1831480.14533240.14734750.9810.98899.91370.139
2.064-2.1760.1481520.13631740.13733270.9860.9999.96990.131
2.176-2.3070.181420.1430120.14231540.9810.9881000.133
2.307-2.4660.1741500.13328290.13529830.9830.98999.86590.127
2.466-2.6630.1671420.14326390.14427820.9830.98799.96410.135
2.663-2.9160.1711460.14424210.14525670.9830.9871000.139
2.916-3.2590.1691220.1522260.15123500.980.98699.91490.147
3.259-3.7590.1541230.1419490.14120730.9860.98899.95180.141
3.759-4.5960.146960.12516770.12617730.9890.9911000.13
4.596-6.4640.194510.15813590.1614100.9820.9881000.164
6.464-44.0570.161550.1688010.1678560.9840.9821000.178

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