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

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Basic information

Entry
Database: PDB / ID: 5xvd
Title[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition
Components
  • Hydrogenase-2 small chain
  • [NiFe]-hydrogenase 2 large subunit
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / 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 / Nickel-dependent hydrogenases large subunit signature 2. ...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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 / IRON/SULFUR CLUSTER / NiFe hydrogenase / hydrogenase (acceptor)
Similarity search - Component
Biological speciesCitrobacter sp. S-77 (bacteria)
Citrobacter sp. MGH106 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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

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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: Hydrogenase-2 small chain
M: [NiFe]-hydrogenase 2 large subunit
T: Hydrogenase-2 small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,22122
Polymers193,6044
Non-polymers3,61818
Water20,1051116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23850 Å2
ΔGint-258 kcal/mol
Surface area44060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.940, 118.980, 96.810
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 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 Hydrogenase-2 small chain


Mass: 35886.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter sp. MGH106 (bacteria) / References: UniProt: A0A0J1PJ79

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Non-polymers , 8 types, 1134 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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: Chemical ChemComp-8JU / FE4-S4-O CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.01 Å3/Da / Density % sol: 34.22 %
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: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 382238 / % possible obs: 97.5 % / Redundancy: 1.9 % / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→31.722 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 9829 5 %
Rwork0.1211 --
obs0.1234 196578 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→31.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12646 0 110 1116 13872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813346
X-RAY DIFFRACTIONf_angle_d1.31418228
X-RAY DIFFRACTIONf_dihedral_angle_d13.7524797
X-RAY DIFFRACTIONf_chiral_restr0.0751984
X-RAY DIFFRACTIONf_plane_restr0.0052373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5699-1.58780.2243300.16516261X-RAY DIFFRACTION100
1.5878-1.60640.24263280.15556230X-RAY DIFFRACTION100
1.6064-1.6260.21643270.14936216X-RAY DIFFRACTION100
1.626-1.64660.20543320.13776310X-RAY DIFFRACTION100
1.6466-1.66830.18953250.13096178X-RAY DIFFRACTION100
1.6683-1.69110.21283300.13196257X-RAY DIFFRACTION100
1.6911-1.71530.20793290.12516256X-RAY DIFFRACTION100
1.7153-1.74090.20523280.11666226X-RAY DIFFRACTION100
1.7409-1.76810.17053300.11096278X-RAY DIFFRACTION100
1.7681-1.79710.16923290.10576240X-RAY DIFFRACTION100
1.7971-1.8280.15633300.09556285X-RAY DIFFRACTION100
1.828-1.86130.1543270.09316211X-RAY DIFFRACTION100
1.8613-1.89710.16673300.0976269X-RAY DIFFRACTION100
1.8971-1.93580.17473300.10026262X-RAY DIFFRACTION100
1.9358-1.97790.14953260.09126205X-RAY DIFFRACTION100
1.9779-2.02390.15663310.09136282X-RAY DIFFRACTION100
2.0239-2.07450.1463270.09276217X-RAY DIFFRACTION100
2.0745-2.13060.15123300.09416266X-RAY DIFFRACTION100
2.1306-2.19320.14523270.09176213X-RAY DIFFRACTION100
2.1932-2.2640.14593280.09856224X-RAY DIFFRACTION100
2.264-2.34490.16513270.10366229X-RAY DIFFRACTION100
2.3449-2.43880.17093290.11276236X-RAY DIFFRACTION99
2.4388-2.54970.15333280.11196244X-RAY DIFFRACTION99
2.5497-2.68410.14353270.11426206X-RAY DIFFRACTION99
2.6841-2.85210.17343280.11976230X-RAY DIFFRACTION99
2.8521-3.07220.16953260.13026200X-RAY DIFFRACTION99
3.0722-3.3810.16213240.12856163X-RAY DIFFRACTION98
3.381-3.86950.15823220.12786100X-RAY DIFFRACTION97
3.8695-4.87240.16243210.13416105X-RAY DIFFRACTION97
4.8724-31.72870.16713230.16936150X-RAY DIFFRACTION96

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