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- PDB-8aio: CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) -

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Basic information

Entry
Database: PDB / ID: 8aio
TitleCO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI)
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / CO-bound
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 only hydrogenase large subunit, C-terminal domain ...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
FE2/S2 (INORGANIC) CLUSTER / Chem-MHX / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsDuan, J. / Hofmann, E. / Happe, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway.
Authors: Duan, J. / Hemschemeier, A. / Burr, D.J. / Stripp, S.T. / Hofmann, E. / Happe, T.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 2.0Mar 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)134,50622
Polymers130,2232
Non-polymers4,28320
Water14,898827
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25311
Polymers65,1111
Non-polymers2,14110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25311
Polymers65,1111
Non-polymers2,14110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.600, 72.160, 103.210
Angle α, β, γ (deg.)90.000, 101.940, 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: 65111.410 Da / Num. of mol.: 2 / Fragment: complete enzyme
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, 847 molecules

#2: Chemical ChemComp-MHX / Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)


Mass: 382.963 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5Fe2N3O4S2
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Mes-NaOH(pH6.0), 0.4M MgCl2, 19%PEG4000, 21%glycerol
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7491 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7491 Å / Relative weight: 1
ReflectionResolution: 1.52→40.03 Å / Num. obs: 193296 / % possible obs: 99.9 % / Redundancy: 7.004 % / Biso Wilson estimate: 19.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.105 / Χ2: 0.857 / Net I/σ(I): 10.53 / Num. measured all: 1353904 / Scaling rejects: 190
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
1.52-1.567.1771.7031.0210239114265142670.5731.836100
1.56-1.67.1411.3691.39900713874138650.6791.47799.9
1.6-1.657.1011.0451.759589413510135040.8031.128100
1.65-1.77.0270.8472.179195113095130860.8250.91599.9
1.7-1.766.9420.652.798853412760127530.9070.70399.9
1.76-1.826.7610.5083.498306512288122850.9310.55100
1.82-1.896.3560.3634.637543311870118680.9550.396100
1.89-1.966.70.2925.997660711440114340.9710.31799.9
1.96-2.057.1050.2397.637792710971109680.9820.258100
2.05-2.157.4110.1889.837773510497104890.9890.20299.9
2.15-2.277.4010.15212.097405010008100060.9930.163100
2.27-2.47.3370.12614.369418946394610.9940.136100
2.4-2.577.2650.11215.7564631890288960.9950.12199.9
2.57-2.787.1560.09518.1659123826582620.9960.103100
2.78-3.046.9750.07621.6853195762776260.9970.082100
3.04-3.46.4630.05726.5744682691969140.9980.06299.9
3.4-3.926.2670.04332.6438429614161320.9980.04799.9
3.92-4.817.1580.03839.7537057517851770.9990.041100
4.81-6.87.2550.03740.0729324404840420.9990.0499.9
6.8-40.036.8340.03443.6315451227622610.9990.03799.3

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Processing

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

4xdc


Resolution: 1.52→40.03 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 9659 5 %
Rwork0.1673 183535 -
obs0.1686 193194 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.04 Å2 / Biso mean: 33.3381 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: final / Resolution: 1.52→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8903 0 144 827 9874
Biso mean--22.89 37.94 -
Num. residues----1146
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
1.52-1.540.32643210.335161136434
1.54-1.560.30723210.314661016422
1.56-1.570.31653190.30560566375
1.57-1.590.31823220.286661166438
1.59-1.620.27513200.279560666386
1.62-1.640.3013210.266660956416
1.64-1.660.27473190.258360756394
1.66-1.690.25183200.245860876407
1.69-1.710.25513200.233260746394
1.71-1.740.23493210.214261076428
1.74-1.770.2473210.205660906411
1.77-1.80.2263240.193661426466
1.8-1.840.19943180.182360426360
1.84-1.870.1923230.17861326455
1.87-1.920.20013200.169760896409
1.92-1.960.19923210.167661056426
1.96-2.010.18333210.168661096430
2.01-2.060.19433230.166161546477
2.06-2.120.18333200.148360726392
2.12-2.190.1743230.150561306453
2.19-2.270.18293200.14860916411
2.27-2.360.17383230.144161246447
2.36-2.470.16973230.144461466469
2.47-2.60.18873210.1561056426
2.6-2.760.1853240.157361506474
2.76-2.970.17063220.154861156437
2.98-3.270.19193260.156861786504
3.27-3.750.18523230.144961476470
3.75-4.720.1553270.134662146541
4.72-40.030.18313320.170463106642

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