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- PDB-6gm2: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D -

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Basic information

Entry
Database: PDB / ID: 6gm2
Title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D
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: 2.76 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 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Jan 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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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)134,09415
Polymers130,1952
Non-polymers3,89913
Water1,36976
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0357
Polymers65,0971
Non-polymers1,9376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0598
Polymers65,0971
Non-polymers1,9627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.870, 72.820, 102.910
Angle α, β, γ (deg.)90.000, 96.860, 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: 65097.379 Da / Num. of mol.: 2 / Mutation: E282D
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, 89 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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97863 Å / Relative weight: 1
ReflectionResolution: 2.76→47.88 Å / Num. obs: 34211 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 2.58 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.222 / Χ2: 0.895 / Net I/σ(I): 8.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.76-2.830.772.0425230.7030.868100
2.83-2.910.6712.4524530.7860.75399.8
2.91-2.990.5912.8423740.8370.66100
2.99-3.090.563323020.8560.628100
3.09-3.190.4693.5722490.8710.52399.9
3.19-3.30.3744.3922010.9140.417100
3.3-3.420.3045.4420830.9440.3499.8
3.42-3.560.2536.2219970.9570.28499.9
3.56-3.720.2067.4919590.9690.232100
3.72-3.90.1789.1118550.980.19899.6
3.9-4.110.13911.1417710.9880.15599.9
4.11-4.360.1212.7316610.990.13499.8
4.36-4.670.10613.8915720.9910.11899.8
4.67-5.040.10613.4514740.990.11899.8
5.04-5.520.10812.2313590.9910.122100
5.52-6.170.11412.2912210.9910.12799.8
6.17-7.130.09415.1910930.9930.10599.8
7.13-8.730.07518.129260.9960.084100
8.73-12.340.05224.317300.9970.05999.7
12.34-47.880.04628.474080.9980.05297.4

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Processing

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

4xdc


Resolution: 2.76→47.88 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1723 5.04 %Random selection
Rwork0.2206 ---
obs0.2234 34206 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.09 Å2 / Biso mean: 34.5591 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 2.76→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8934 0 107 76 9117
Biso mean--25.42 26.57 -
Num. residues----1150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049278
X-RAY DIFFRACTIONf_angle_d0.77912456
X-RAY DIFFRACTIONf_chiral_restr0.0311358
X-RAY DIFFRACTIONf_plane_restr0.0041608
X-RAY DIFFRACTIONf_dihedral_angle_d14.0343446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7601-2.84140.34261380.298326902828
2.8414-2.93310.36151400.284626902830
2.9331-3.03790.29431220.271727082830
3.0379-3.15950.31371360.27826942830
3.1595-3.30320.34161590.255126962855
3.3032-3.47730.28121590.230326582817
3.4773-3.69510.28821520.224626832835
3.6951-3.98030.25561320.217127182850
3.9803-4.38060.26631440.195627052849
4.3806-5.01390.24621340.186827272861
5.0139-6.31470.25561680.20527012869
6.3147-47.88740.21391390.167928132952

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