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- PDB-5xvb: [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-... -

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Basic information

Entry
Database: PDB / ID: 5xvb
Title[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition
Components([NiFe]-hydrogenase 2 ...) x 2
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / hydrogenase (acceptor) / Hydrogenase-2 small chain
Similarity search - Component
Biological speciesCitrobacter sp. S-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNishikawa, K. / Matsuura, H. / Muhd Noor, N.D. / Tai, H. / Hirota, S. / Kim, J. / Kang, J. / Tateno, M. / Yoon, K.S. / Ogo, S. ...Nishikawa, K. / Matsuura, H. / Muhd Noor, N.D. / Tai, H. / Hirota, S. / Kim, J. / Kang, J. / Tateno, M. / Yoon, K.S. / Ogo, S. / Shomura, Y. / Higuchi, Y.
CitationJournal: Chem.Commun.(Camb.) / Year: 2018
Title: Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.
Authors: Noor, N.D.M. / Matsuura, H. / Nishikawa, K. / Tai, H. / Hirota, S. / Kim, J. / Kang, J. / Tateno, M. / Yoon, K.S. / Ogo, S. / Kubota, S. / Shomura, Y. / Higuchi, Y.
History
DepositionJun 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0Aug 12, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: [NiFe]-hydrogenase 2 large subunit
S: [NiFe]-hydrogenase 2 small subunit
M: [NiFe]-hydrogenase 2 large subunit
T: [NiFe]-hydrogenase 2 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,48320
Polymers196,6794
Non-polymers2,80416
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23650 Å2
ΔGint-240 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 121.610, 98.880
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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[NiFe]-hydrogenase 2 ... , 2 types, 4 molecules LMST

#1: Protein [NiFe]-hydrogenase 2 large subunit


Mass: 62452.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter sp. S-77 (bacteria) / References: UniProt: A0A3B6UEP7*PLUS
#2: Protein [NiFe]-hydrogenase 2 small subunit


Mass: 35886.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter sp. S-77 (bacteria) / References: UniProt: A0A3B6UEQ0*PLUS

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Non-polymers , 7 types, 517 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 18% PEG 10000, 100 mM Sodium Chloride, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 251118 / % possible obs: 96.8 % / Redundancy: 1.9 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→38.02 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 6536 5 %
Rwork0.1806 --
obs0.1826 130761 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12628 0 88 501 13217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113126
X-RAY DIFFRACTIONf_angle_d1.57917906
X-RAY DIFFRACTIONf_dihedral_angle_d14.7184694
X-RAY DIFFRACTIONf_chiral_restr0.0971957
X-RAY DIFFRACTIONf_plane_restr0.0062316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86090.31592170.29794125X-RAY DIFFRACTION100
1.8609-1.88280.34042190.30174158X-RAY DIFFRACTION100
1.8828-1.90570.35492160.29284093X-RAY DIFFRACTION100
1.9057-1.92990.32872190.29184163X-RAY DIFFRACTION100
1.9299-1.95530.31132140.26754074X-RAY DIFFRACTION100
1.9553-1.9820.31742180.25524144X-RAY DIFFRACTION100
1.982-2.01040.29232170.24214120X-RAY DIFFRACTION100
2.0104-2.04040.26722160.22424139X-RAY DIFFRACTION100
2.0404-2.07220.30292170.23774118X-RAY DIFFRACTION99
2.0722-2.10620.27672160.21714119X-RAY DIFFRACTION100
2.1062-2.14250.26372170.20644127X-RAY DIFFRACTION100
2.1425-2.18150.24222200.20334179X-RAY DIFFRACTION100
2.1815-2.22340.24222150.19924084X-RAY DIFFRACTION100
2.2234-2.26880.27062180.20644138X-RAY DIFFRACTION99
2.2688-2.31820.25322180.19194122X-RAY DIFFRACTION100
2.3182-2.37210.22962170.18594131X-RAY DIFFRACTION100
2.3721-2.43140.23412180.18094141X-RAY DIFFRACTION100
2.4314-2.49710.23362170.17854116X-RAY DIFFRACTION100
2.4971-2.57060.23212200.17744176X-RAY DIFFRACTION100
2.5706-2.65350.23752180.18664152X-RAY DIFFRACTION100
2.6535-2.74830.25242180.18244128X-RAY DIFFRACTION100
2.7483-2.85830.19792180.17674142X-RAY DIFFRACTION100
2.8583-2.98840.22682190.18154176X-RAY DIFFRACTION100
2.9884-3.14590.21232170.17884112X-RAY DIFFRACTION100
3.1459-3.34280.21872190.1754157X-RAY DIFFRACTION100
3.3428-3.60080.19522170.16394136X-RAY DIFFRACTION100
3.6008-3.96280.18522200.15094182X-RAY DIFFRACTION100
3.9628-4.53540.15742190.13214153X-RAY DIFFRACTION100
4.5354-5.7110.15542210.14064192X-RAY DIFFRACTION100
5.711-38.02850.16142210.15124228X-RAY DIFFRACTION99

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