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- PDB-6gm8: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q -

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Basic information

Entry
Database: PDB / ID: 6gm8
Title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / Hydrogenase / H-cluster / semisynthetic enzyme
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #740 / : / 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 ...Ubiquitin-like (UB roll) - #740 / : / 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 / Alpha-Beta Plaits - #20 / 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 / Ubiquitin-like (UB roll) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
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: 1.96 Å
AuthorsDuan, J. / Esselborn, J. / Hofmann, E. / Winkler, M. / Happe, T.
CitationJournal: Nat Commun / Year: 2018
Title: Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases.
Authors: Duan, J. / Senger, M. / Esselborn, J. / Engelbrecht, V. / Wittkamp, F. / Apfel, U.P. / Hofmann, E. / Stripp, S.T. / Happe, T. / Winkler, M.
History
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)134,16817
Polymers130,2212
Non-polymers3,94815
Water15,637868
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0969
Polymers65,1101
Non-polymers1,9868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0728
Polymers65,1101
Non-polymers1,9627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.650, 72.340, 103.150
Angle α, β, γ (deg.)90.000, 96.730, 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: 65110.426 Da / Num. of mol.: 2 / Mutation: E282Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DiscR / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 5 types, 883 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
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00006 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00006 Å / Relative weight: 1
ReflectionResolution: 1.96→47.769 Å / Num. obs: 92827 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Biso Wilson estimate: 24.22 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.158 / Rsym value: 0.162 / Net I/σ(I): 7.93
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.96-2.010.911.99197.5
2.01-2.070.7442.49197.4
2.07-2.130.6153.16198.1
2.13-2.190.5153.68197.7
2.19-2.260.444.28198.1
2.26-2.340.3695198.1
2.34-2.430.3125.73198.4
2.43-2.530.2856198.5
2.53-2.640.2396.87198.5
2.64-2.770.218.2198.8
2.77-2.920.1789.45199
2.92-3.10.15410.74198.9
3.1-3.310.13312.14199.1
3.31-3.580.11513.47199.1
3.58-3.920.09814.45199.1
3.92-4.380.0917.16199.4
4.38-5.060.08717.78199.4
5.06-6.20.08717.02199.3
6.2-8.770.08417.41199.3
8.77-47.770.07619.86199

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDC

4xdc


Resolution: 1.96→46.832 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 4674 5.04 %Random selection
Rwork0.1763 ---
obs0.1786 92798 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.43 Å2 / Biso mean: 31.8459 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.96→46.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8961 0 109 868 9938
Biso mean--20.52 41.05 -
Num. residues----1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119314
X-RAY DIFFRACTIONf_angle_d1.12512491
X-RAY DIFFRACTIONf_chiral_restr0.0511362
X-RAY DIFFRACTIONf_plane_restr0.0051612
X-RAY DIFFRACTIONf_dihedral_angle_d13.8313457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.98230.30841720.24742848302097
1.9823-2.00560.28131520.22542922307498
2.0056-2.03010.25091560.20792850300697
2.0301-2.05580.25161350.1932937307298
2.0558-2.08280.25611280.1842916304498
2.0828-2.11140.23691700.17882863303398
2.1114-2.14150.23851510.17522946309798
2.1415-2.17350.20821590.17552921308098
2.1735-2.20750.25471470.16852870301798
2.2075-2.24370.21821560.16352936309298
2.2437-2.28230.20481600.16692875303599
2.2823-2.32380.22491520.16112936308898
2.3238-2.36850.24241530.15962922307598
2.3685-2.41690.22111450.16412961310698
2.4169-2.46940.22441570.16632893305098
2.4694-2.52690.21871610.1712925308698
2.5269-2.59010.2371560.16152928308499
2.5901-2.66010.22891510.17012953310499
2.6601-2.73830.21641650.17452959312499
2.7383-2.82670.23841670.18112899306699
2.8267-2.92770.25541480.17792993314199
2.9277-3.04490.23241320.17932945307799
3.0449-3.18350.20881570.18052952310999
3.1835-3.35130.21221830.17052961314499
3.3513-3.56120.20081690.16632946311599
3.5612-3.8360.20611610.17442983314499
3.836-4.22180.1961470.16372983313099
4.2218-4.83220.17781550.16333008316399
4.8322-6.0860.25131740.19042998317299
6.086-46.84570.21251550.19793095325099

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