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- PDB-8cjy: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T -

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Basic information

Entry
Database: PDB / ID: 8cjy
Title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / CpI from Clostridium pasteurianum / variant S357T
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, 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 ...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: 1.6 Å
AuthorsBrocks, C. / Duan, J. / Hofmann, E. / Happe, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2341 Germany
CitationJournal: Chemsuschem / Year: 2024
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
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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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)134,54924
Polymers130,2512
Non-polymers4,29822
Water10,971609
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,27412
Polymers65,1251
Non-polymers2,14911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,27412
Polymers65,1251
Non-polymers2,14911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.730, 72.290, 103.040
Angle α, β, γ (deg.)90.00, 96.95, 90.00
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: 65125.434 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 , 7 types, 631 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1M Mes pH6.0, 20% PEG4000, 20% glycerol, 0.4M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 1, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→44.54 Å / Num. obs: 169895 / % possible obs: 98.5 % / Redundancy: 7.13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.11 / Net I/σ(I): 10.42
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.642.023124530.4592.1731
1.64-1.691.661121780.5441.7851
1.69-1.741.264118590.6921.3591
1.74-1.791.009115780.7781.0851
1.79-1.850.784112770.8430.8441
1.85-1.910.552109020.9180.5941
1.91-1.980.441104980.9440.4761
1.98-2.070.346101530.9650.3731
2.07-2.160.26296530.9780.2831
2.16-2.260.20492960.9870.2211
2.26-2.390.16387890.990.1761
2.39-2.530.13381820.9910.1461
2.53-2.70.10670460.9940.1151
2.7-2.920.0973540.9960.0971
2.92-3.20.07368360.9970.0781
3.2-3.580.05661640.9980.0611
3.58-4.130.04654380.9990.051
4.13-5.060.04146240.9990.0441
5.06-7.160.04336080.9990.0461
7.16-44.540.04120070.9980.0451

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.1_4122refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 8493 5 %
Rwork0.1639 --
obs0.165 169865 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8954 0 126 609 9689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079296
X-RAY DIFFRACTIONf_angle_d0.83712553
X-RAY DIFFRACTIONf_dihedral_angle_d15.0673481
X-RAY DIFFRACTIONf_chiral_restr0.0511366
X-RAY DIFFRACTIONf_plane_restr0.0071623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.36672780.3485280X-RAY DIFFRACTION98
1.62-1.640.36232820.32995362X-RAY DIFFRACTION98
1.64-1.660.31132800.32285316X-RAY DIFFRACTION98
1.66-1.680.31642820.29335370X-RAY DIFFRACTION99
1.68-1.70.31952820.27985366X-RAY DIFFRACTION99
1.7-1.720.28762840.26675388X-RAY DIFFRACTION99
1.72-1.750.28452810.2535349X-RAY DIFFRACTION99
1.75-1.770.27022850.23795404X-RAY DIFFRACTION99
1.77-1.80.23312820.23165365X-RAY DIFFRACTION99
1.8-1.830.25112840.21665402X-RAY DIFFRACTION99
1.83-1.860.21032840.20835383X-RAY DIFFRACTION99
1.86-1.90.21122840.18455388X-RAY DIFFRACTION99
1.9-1.930.21772840.17745398X-RAY DIFFRACTION99
1.93-1.970.20232840.175395X-RAY DIFFRACTION99
1.97-2.020.18672840.1635402X-RAY DIFFRACTION99
2.02-2.060.18732860.15465435X-RAY DIFFRACTION99
2.06-2.110.15072820.14675353X-RAY DIFFRACTION99
2.11-2.170.18932870.14775448X-RAY DIFFRACTION99
2.17-2.240.16232820.15155371X-RAY DIFFRACTION99
2.24-2.310.18052870.14785435X-RAY DIFFRACTION99
2.31-2.390.18222820.14345369X-RAY DIFFRACTION99
2.39-2.490.17712820.14065345X-RAY DIFFRACTION98
2.49-2.60.18372500.14824751X-RAY DIFFRACTION87
2.6-2.740.1912750.15235223X-RAY DIFFRACTION95
2.74-2.910.19322870.15785457X-RAY DIFFRACTION100
2.91-3.130.18822890.1545497X-RAY DIFFRACTION100
3.13-3.450.17582880.15165478X-RAY DIFFRACTION100
3.45-3.940.16052900.14045500X-RAY DIFFRACTION100
3.94-4.970.14692900.13185520X-RAY DIFFRACTION100
4.97-39.330.16782960.16455622X-RAY DIFFRACTION100

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