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Basic information

Entry
Database: PDB / ID: 5xlg
TitleCrystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase D. vulgaris
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding
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 / 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
FE3-S4 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / Periplasmic [NiFe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsNishikawa, K. / Mochida, S. / Hiromoto, T. / Shibata, N. / Higuchi, Y.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Authors: Nishikawa, K. / Mochida, S. / Hiromoto, T. / Shibata, N. / Higuchi, Y.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
S: Periplasmic [NiFe] hydrogenase small subunit
L: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2429
Polymers89,7682
Non-polymers1,4747
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-113 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.590, 98.960, 127.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules SL

#1: Protein Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28789.746 Da / Num. of mol.: 1 / Fragment: UNP residues 51-317 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) (bacteria)
Strain: Miyazaki F / DSM 19637 / References: UniProt: P21853, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 60978.453 Da / Num. of mol.: 1 / Fragment: UNP residues 1-552 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) (bacteria)
Strain: Miyazaki F / DSM 19637 / References: UniProt: P21852, cytochrome-c3 hydrogenase

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Non-polymers , 7 types, 831 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3FeN2NiO2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 194340 / % possible obs: 99.9 % / Redundancy: 3.6 % / Net I/σ(I): 16.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→39.01 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1668 5102 5 %
Rwork0.1408 --
obs0.1421 102030 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 49 824 7053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116486
X-RAY DIFFRACTIONf_angle_d1.6468851
X-RAY DIFFRACTIONf_dihedral_angle_d15.562347
X-RAY DIFFRACTIONf_chiral_restr0.086955
X-RAY DIFFRACTIONf_plane_restr0.0071152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65860.27621530.26072911X-RAY DIFFRACTION88
1.6586-1.67810.27591600.24183036X-RAY DIFFRACTION93
1.6781-1.69860.27761640.22563115X-RAY DIFFRACTION97
1.6986-1.72010.23821660.1913158X-RAY DIFFRACTION98
1.7201-1.74270.21831680.17363183X-RAY DIFFRACTION98
1.7427-1.76660.19181670.16373184X-RAY DIFFRACTION98
1.7666-1.79190.18421670.15263181X-RAY DIFFRACTION98
1.7919-1.81860.16691690.14653195X-RAY DIFFRACTION99
1.8186-1.8470.19661670.15063188X-RAY DIFFRACTION98
1.847-1.87730.18931690.14823195X-RAY DIFFRACTION99
1.8773-1.90970.18721670.15963188X-RAY DIFFRACTION98
1.9097-1.94440.19331710.15393233X-RAY DIFFRACTION99
1.9444-1.98180.17511690.14493209X-RAY DIFFRACTION99
1.9818-2.02220.15391710.13673258X-RAY DIFFRACTION98
2.0222-2.06620.15251680.12773190X-RAY DIFFRACTION99
2.0662-2.11430.16261690.1323222X-RAY DIFFRACTION99
2.1143-2.16710.17041710.13253242X-RAY DIFFRACTION99
2.1671-2.22570.17351710.1323238X-RAY DIFFRACTION99
2.2257-2.29120.16971720.13383282X-RAY DIFFRACTION100
2.2912-2.36520.17351710.13523238X-RAY DIFFRACTION100
2.3652-2.44970.1771710.12883263X-RAY DIFFRACTION99
2.4497-2.54770.16461730.12843285X-RAY DIFFRACTION100
2.5477-2.66370.15491730.13133284X-RAY DIFFRACTION100
2.6637-2.80410.16241710.13093254X-RAY DIFFRACTION100
2.8041-2.97970.15451750.1323317X-RAY DIFFRACTION100
2.9797-3.20970.1441740.13053315X-RAY DIFFRACTION100
3.2097-3.53250.14011760.12223329X-RAY DIFFRACTION100
3.5325-4.04320.13511750.12093340X-RAY DIFFRACTION100
4.0432-5.09220.13421790.12153394X-RAY DIFFRACTION100
5.0922-39.02060.18411850.17443501X-RAY DIFFRACTION99

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