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- PDB-5xvc: [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in a ferr... -

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Basic information

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


hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin 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) / [Ni-Fe] hydrogenase complex / ferredoxin 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 / membrane / 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 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / [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. / [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
FE4-S4-O CLUSTER / FE3-S4 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / hydrogenase (acceptor) / hydrogenase (acceptor)
Similarity search - Component
Biological speciesCitrobacter sp. S-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr2_label_seq_id / _struct_conn_type.id

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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)196,21015
Polymers193,6044
Non-polymers2,60611
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21890 Å2
ΔGint-187 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.970, 121.830, 99.170
Angle α, β, γ (deg.)90.00, 102.93, 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: 60915.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter sp. S-77 (bacteria) / References: UniProt: A0A3B6UEQ1*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, 526 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-8JU / FE4-S4-O CLUSTER


Mass: 367.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4OS4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.16 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 18% PEG 10000, 100mM 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: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 184162 / % possible obs: 97.5 % / Redundancy: 2 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→37.86 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 4744 5 %
Rwork0.1659 --
obs0.1685 94895 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12632 0 75 515 13222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113097
X-RAY DIFFRACTIONf_angle_d1.31917848
X-RAY DIFFRACTIONf_dihedral_angle_d15.8854705
X-RAY DIFFRACTIONf_chiral_restr0.0931956
X-RAY DIFFRACTIONf_plane_restr0.0062312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.27271570.2372992X-RAY DIFFRACTION99
2.0733-2.09770.31021560.22492947X-RAY DIFFRACTION98
2.0977-2.12330.29551580.21263010X-RAY DIFFRACTION99
2.1233-2.15010.26261550.20662943X-RAY DIFFRACTION99
2.1501-2.17840.28381570.20692968X-RAY DIFFRACTION99
2.1784-2.20830.24371590.19373028X-RAY DIFFRACTION99
2.2083-2.23980.26581550.19632947X-RAY DIFFRACTION99
2.2398-2.27320.29811590.19263013X-RAY DIFFRACTION99
2.2732-2.30880.2571570.19643005X-RAY DIFFRACTION99
2.3088-2.34660.25841580.18762989X-RAY DIFFRACTION99
2.3466-2.38710.2631550.19272948X-RAY DIFFRACTION99
2.3871-2.43050.24711580.1852997X-RAY DIFFRACTION99
2.4305-2.47720.23831580.17863008X-RAY DIFFRACTION99
2.4772-2.52770.25171580.1823015X-RAY DIFFRACTION99
2.5277-2.58270.23921550.18292953X-RAY DIFFRACTION99
2.5827-2.64280.26171610.18013049X-RAY DIFFRACTION100
2.6428-2.70880.23681570.17392991X-RAY DIFFRACTION99
2.7088-2.78210.23271570.16472982X-RAY DIFFRACTION100
2.7821-2.86390.19931590.16973019X-RAY DIFFRACTION99
2.8639-2.95630.2421590.17773018X-RAY DIFFRACTION100
2.9563-3.06190.23931580.16843004X-RAY DIFFRACTION100
3.0619-3.18440.23951590.17763032X-RAY DIFFRACTION100
3.1844-3.32930.2161590.16813009X-RAY DIFFRACTION100
3.3293-3.50470.21761590.16183023X-RAY DIFFRACTION100
3.5047-3.72410.1771590.15523014X-RAY DIFFRACTION100
3.7241-4.01140.16571590.13793021X-RAY DIFFRACTION100
4.0114-4.41450.16951610.12863067X-RAY DIFFRACTION100
4.4145-5.0520.15141600.12153039X-RAY DIFFRACTION100
5.052-6.36010.19251590.14573031X-RAY DIFFRACTION100
6.3601-37.86650.16551630.14133089X-RAY DIFFRACTION99

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