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- PDB-7qhf: [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant... -

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Basic information

Entry
Database: PDB / ID: 7qhf
Title[FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant G302S
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) / variant G302S
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
: / Iron hydrogenase 1-like, iron-sulfur centre-binding domain / 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 hydrogenase 1-like, iron-sulfur centre-binding domain / 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 / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBrocks, C. / Duan, J. / Hofmann, E. / Happe, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2341 Germany
CitationJournal: Chemsuschem / Year: 2023
Title: A Dynamic Water Channel Affects O 2 Stability in [FeFe]-Hydrogenases.
Authors: Brocks, C. / Das, C.K. / Duan, J. / Yadav, S. / Apfel, U.P. / Ghosh, S. / Hofmann, E. / Winkler, M. / Engelbrecht, V. / Schafer, L.V. / Happe, T.
History
DepositionDec 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron hydrogenase 1
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,43920
Polymers130,2832
Non-polymers4,15618
Water15,925884
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21910
Polymers65,1411
Non-polymers2,0789
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21910
Polymers65,1411
Non-polymers2,0789
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.490, 72.220, 102.920
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iron hydrogenase 1 / CpI / Fe-only hydrogenase / [Fe] hydrogenase


Mass: 65141.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 6 types, 902 molecules

#2: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1M Mes-NaOH (pH 6.0), 0.4 M MgCl2, 20% PEG4000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.63→47.53 Å / Num. obs: 162137 / % possible obs: 99.9 % / Redundancy: 6.489 % / Biso Wilson estimate: 24.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.125 / Χ2: 0.849 / Net I/σ(I): 7.87 / Num. measured all: 1052087 / Scaling rejects: 127
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.676.5161.521.017771311930119270.5021.652100
1.67-1.726.4241.2211.297509911693116900.6411.329100
1.72-1.776.180.9461.656978011305112910.7261.03399.9
1.77-1.826.4390.7642.127086911008110070.8080.831100
1.82-1.886.4270.5552.926838010645106400.8910.604100
1.88-1.956.5770.4343.786831110388103860.9260.471100
1.95-2.026.4880.3574.5664366992499210.950.389100
2.02-2.16.1760.2745.6758898954795370.9660.29999.9
2.1-2.26.4440.2257.0259330921392070.9740.24599.9
2.2-2.316.480.1878.4657161883088210.9820.20399.9
2.31-2.436.8470.15910.0457303836583690.9870.172100
2.43-2.586.7620.1411.2653848797279630.9890.15299.9
2.58-2.766.5010.1212.6648358744274390.990.13100
2.76-2.986.5890.10514.6445727693869400.9910.114100
2.98-3.266.8660.09317.1244055642164160.9930.199.9
3.26-3.646.6880.0819.1838772580357970.9940.08799.9
3.64-4.216.4180.07420.3232931514051310.9940.08199.8
4.21-5.156.5180.07321.3428406435943580.9920.079100
5.15-7.296.2260.07320.6221120339933920.9940.0899.8
7.29-47.536.1210.07421.5911660192219050.9940.08199.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDC

4xdc


Resolution: 1.63→47.53 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 8109 5 %
Rwork0.1694 154002 -
obs0.1705 162111 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.13 Å2 / Biso mean: 34.4586 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 1.63→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8938 0 122 884 9944
Biso mean--25.14 41.51 -
Num. residues----1150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.63-1.650.37742490.357251165365
1.65-1.670.35612560.325550915347
1.67-1.690.32252630.318351755438
1.69-1.710.30632390.29450835322
1.71-1.730.29922800.267150885368
1.73-1.760.28642630.25551505413
1.76-1.780.28112590.241350715330
1.78-1.810.27222590.231851585417
1.81-1.840.22832630.211851155378
1.84-1.870.22982970.199850885385
1.87-1.90.21092890.193550915380
1.9-1.930.23022800.197551205400
1.93-1.970.22572870.188850705357
1.97-2.010.2092660.179251485414
2.01-2.050.19942580.166451555413
2.05-2.10.19272710.154651125383
2.1-2.150.18632610.1651155376
2.15-2.210.18922770.160251215398
2.21-2.280.20372770.162651165393
2.28-2.350.19852780.158451395417
2.35-2.430.21222570.162351305387
2.43-2.530.21512710.168551375408
2.53-2.650.20282710.166951395410
2.65-2.790.18492860.165351595445
2.79-2.960.21142670.16851365403
2.96-3.190.17512480.16551815429
3.19-3.510.15483140.152751125426
3.51-4.020.15962640.14151925456
4.02-5.060.15472680.1452065474
5.06-47.530.17262910.164252885579

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