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- PDB-1h2r: THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBR... -

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Basic information

Entry
Database: PDB / ID: 1h2r
TitleTHREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION
Components(PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / HIGH RESOLUTION CRYSTAL STRUCTURE / SULFUR-BRIDGING LIGAND / NI-FE HYDROGENASE / REDUCED ENZYME / ATOMIC CAP AT ACTIVE SITE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / 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 / 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
FE3-S4 CLUSTER / NI-FE ACTIVE CENTER / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / Periplasmic [NiFe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / D-FOURIER / Resolution: 1.4 Å
AuthorsHiguchi, Y. / Ogata, H.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.
Authors: Higuchi, Y. / Ogata, H. / Miki, K. / Yasuoka, N. / Yagi, T.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1999
Title: Liberation of Hydrogen Sulfide During the Catalytic Action of Desulfoviborio Hydrogenase Under the Atmosphere of Hydrogen
Authors: Higuchi, Y. / Yagi, T.
#2: Journal: Structure / Year: 1997
Title: Unusual Ligand Structure in Ni-Fe Active Center and an Additional Mg Site in Hydrogenase Revealed by High Resolution X-Ray Structure Analysis
Authors: Higuchi, Y. / Yagi, T. / Yasuoka, N.
History
DepositionJun 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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 / struct_site
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_asym_id / _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_asym_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_asym_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.ptnr3_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)
L: PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2447
Polymers87,9692
Non-polymers1,2755
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-113 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.440, 126.860, 66.680
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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PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE ... , 2 types, 2 molecules SL

#1: Protein PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) / HYDROGEN: FERRICYTOCHROME-C3 OXIDOREDUCTASE


Mass: 28789.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Cellular location: PERIPLASMIC MEMBRANE / Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P21853, cytochrome-c3 hydrogenase
#2: Protein PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT) / HYDROGEN: FERRICYTOCHROME-C3 OXIDOREDUCTASE


Mass: 59179.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Cellular location: PERIPLASMIC MEMBRANE / Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P21852, cytochrome-c3 hydrogenase

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Non-polymers , 5 types, 582 molecules

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


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NFE / NI-FE ACTIVE CENTER


Mass: 251.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HFeNiO3S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: 45% MPD, pH 7.0
Crystal grow
*PLUS
pH: 7.4 / Method: microdialysis / Details: Higuchi, Y., (1987) J.Biol.Chem., 262, 2823.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140 mg/mlprotein11
225 mMTris-HCl11
320 mM11NaCl
420 %(w/v)PEG12
520 %(w/v)sodium citrate12
640 %satammonium sulfate12
740 %(v/v)ethanol12
840 %(v/v)MPD12or 1M NaCl

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 155198 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.036
Reflection shellResolution: 1.4→1.46 Å / Rmerge(I) obs: 0.38 / Rsym value: 0.3 / % possible all: 85.1
Reflection
*PLUS
Num. measured all: 1453748
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
PROTEINmodel building
MLPHARE(CCP4)phasing
X-PLORrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
PROTEINphasing
RefinementMethod to determine structure: D-FOURIER
Starting model: 1H2A

1h2a


Resolution: 1.4→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.254 10200 7 %
Rwork0.218 --
obs0.218 145719 86 %
Displacement parametersBiso mean: 17.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6194 0 32 577 6803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.96
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.4→1.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 900 7 %
Rwork0.306 13676 -
obs--66 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 6 Å / σ(F): 1 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.8 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / % reflection Rfree: 7 % / Rfactor Rwork: 0.306 / Rfactor obs: 0.306

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