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- PDB-5byq: Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [... -

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Basic information

Entry
Database: PDB / ID: 5byq
TitleSemisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor
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, 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 ...Ubiquitin-like (UB roll) - #740 / 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-4WV / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsEsselborn, J. / Muraki, N. / Engelbrecht, V. / Hofmann, E. / Kurisu, G. / Happe, T.
CitationJournal: Chem Sci / Year: 2016
Title: A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.
Authors: Esselborn, J. / Muraki, N. / Klein, K. / Engelbrecht, V. / Metzler-Nolte, N. / Apfel, U.P. / Hofmann, E. / Kurisu, G. / Happe, T.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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 / _citation_author.name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Jan 10, 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)134,38120
Polymers130,2232
Non-polymers4,15818
Water15,745874
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19010
Polymers65,1111
Non-polymers2,0799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19010
Polymers65,1111
Non-polymers2,0799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.660, 72.450, 102.940
Angle α, β, γ (deg.)90.000, 96.760, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pET21b / Details (production host): C-terminal strep-tagII / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DiscR / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 6 types, 892 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-4WV / bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) / oxodithiolato-bridged [2Fe2S] cluster


Mass: 355.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4Fe2N2O4S2
#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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 19% PEG 4000, 0.4 M MgCl,0.1 M MES, 21 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→47.77 Å / Num. obs: 136702 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 21.49 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.087 / Χ2: 0.996 / Net I/σ(I): 14.13 / Num. measured all: 929911
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.73-1.770.8410.7682.077057510136101320.831100
1.77-1.820.8770.6392.5567279973197390.692100
1.82-1.880.9260.4883.3765230955895500.52899.9
1.88-1.930.9460.3964.1862526928292830.43100
1.93-20.9550.3284.9957276899189870.358100
2-2.070.9730.2686.2657988869687000.291100
2.07-2.150.9830.2118.1459251837983750.228100
2.15-2.230.9870.1729.9156961809480960.186100
2.23-2.330.990.14811.6454297779577910.1699.9
2.33-2.450.9920.12613.4350514736973690.136100
2.45-2.580.9940.10814.8445477710170930.11899.9
2.58-2.740.9950.09418.0646147666066610.102100
2.74-2.920.9970.07621.844983627762780.082100
2.92-3.160.9970.06425.8141320587458730.069100
3.16-3.460.9980.05230.9536464540253970.05699.9
3.46-3.870.9980.04334.4830017489948960.04799.9
3.87-4.470.9990.03641.7730280433943410.039100
4.47-5.470.9990.03542.2525157367036670.03899.9
5.47-7.740.9990.03739.9517527286828630.04199.8
7.740.9990.03347.9710642162016110.03699.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xdc

4xdc


Resolution: 1.73→47.77 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 1442 1.06 %Inherited from MR model
Rwork0.1464 135224 --
obs0.1467 136666 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.2 Å2 / Biso mean: 35.7165 Å2 / Biso min: 14.09 Å2
Refinement stepCycle: final / Resolution: 1.73→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8976 0 138 874 9988
Biso mean--24.59 38.68 -
Num. residues----1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099289
X-RAY DIFFRACTIONf_angle_d1.06912537
X-RAY DIFFRACTIONf_chiral_restr0.0411366
X-RAY DIFFRACTIONf_plane_restr0.0051617
X-RAY DIFFRACTIONf_dihedral_angle_d13.7573465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.73-1.79180.29281440.24511342313567
1.7918-1.86360.23591430.21011349013633
1.8636-1.94840.18561440.17951345813602
1.9484-2.05110.20321430.17011344813591
2.0511-2.17960.17141440.14831348713631
2.1796-2.34790.16421430.13921350113644
2.3479-2.58420.17711450.13991352313668
2.5842-2.95810.19841440.14661352113665
2.9581-3.72660.17711450.14071358113726
3.7266-47.78850.14151470.12451379213939

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