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- PDB-4u9i: High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4u9i
TitleHigh Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / metal-hydride / hydrogenase
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / 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 / 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 / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / HoxL-like / 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 / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / HoxL-like / 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 / 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
NI-FE REDUCED ACTIVE CENTER / FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / Periplasmic [NiFe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsOgata, H. / Nishikawa, K. / Lubitz, W.
Funding support Germany, Belgium, 2items
OrganizationGrant numberCountry
BMBF03SF0355C Germany
EU/Energy Network project SOLAR-H2FP7 contract 212508 Belgium
CitationJournal: Nature / Year: 2015
Title: Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.
Authors: Ogata, H. / Nishikawa, K. / Lubitz, W.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Dec 20, 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
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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Aug 26, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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_site.details / _struct_site.pdbx_auth_comp_id
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
S: Periplasmic [NiFe] hydrogenase small subunit
L: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,93916
Polymers87,6532
Non-polymers2,28714
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-173 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 99.690, 122.190
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: 28545.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / DSM 19637 / References: UniProt: P21853, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59107.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / DSM 19637 / References: UniProt: P21852, cytochrome-c3 hydrogenase

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Non-polymers , 7 types, 794 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.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-EJ2 / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.06→49.2 Å / Num. obs: 648452 / % possible obs: 94.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 1.06→1.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.3 / % possible all: 78.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1388)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUI

1wui


Resolution: 1.06→49.2 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1318 32431 5 %
Rwork0.1099 --
obs0.111 648390 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 104 780 7057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146741
X-RAY DIFFRACTIONf_angle_d1.519237
X-RAY DIFFRACTIONf_dihedral_angle_d16.5272473
X-RAY DIFFRACTIONf_chiral_restr0.095997
X-RAY DIFFRACTIONf_plane_restr0.011211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.07210.28318750.2716765X-RAY DIFFRACTION77
1.0721-1.08470.27468930.246417012X-RAY DIFFRACTION78
1.0847-1.09790.23129220.230517396X-RAY DIFFRACTION81
1.0979-1.11180.23959450.212217837X-RAY DIFFRACTION83
1.1118-1.12640.21379650.199318551X-RAY DIFFRACTION86
1.1264-1.14190.218410210.190919340X-RAY DIFFRACTION89
1.1419-1.15820.205110740.178720415X-RAY DIFFRACTION94
1.1582-1.17550.184610680.173620512X-RAY DIFFRACTION95
1.1755-1.19380.203310900.162420681X-RAY DIFFRACTION95
1.1938-1.21340.179811010.156920732X-RAY DIFFRACTION96
1.2134-1.23430.175211050.153120955X-RAY DIFFRACTION97
1.2343-1.25680.183311050.146721037X-RAY DIFFRACTION97
1.2568-1.2810.173611210.137921111X-RAY DIFFRACTION98
1.281-1.30710.160611080.129521283X-RAY DIFFRACTION98
1.3071-1.33550.14811270.124621237X-RAY DIFFRACTION98
1.3355-1.36660.155411290.120321315X-RAY DIFFRACTION98
1.3666-1.40080.155211290.113221292X-RAY DIFFRACTION98
1.4008-1.43860.141411110.103821302X-RAY DIFFRACTION98
1.4386-1.4810.135211180.099421313X-RAY DIFFRACTION98
1.481-1.52880.123511120.094421189X-RAY DIFFRACTION98
1.5288-1.58340.120111160.091121218X-RAY DIFFRACTION98
1.5834-1.64680.12511180.085921188X-RAY DIFFRACTION98
1.6468-1.72180.115211150.084121282X-RAY DIFFRACTION98
1.7218-1.81260.105411300.077721525X-RAY DIFFRACTION100
1.8126-1.92610.104811420.079921552X-RAY DIFFRACTION100
1.9261-2.07490.094411490.076621581X-RAY DIFFRACTION100
2.0749-2.28370.098111310.07621508X-RAY DIFFRACTION100
2.2837-2.61410.099311350.078621593X-RAY DIFFRACTION100
2.6141-3.29340.104111380.089921628X-RAY DIFFRACTION100
3.2934-49.26650.125611380.121321609X-RAY DIFFRACTION100

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