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- PDB-4u9h: Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrog... -

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Basic information

Entry
Database: PDB / ID: 4u9h
TitleUltra High 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 / 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 / Chem-NWN / 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: 0.89 Å
AuthorsOgata, H. / Nishikawa, K. / Lubitz, W.
Funding support Germany, Belgium, 2items
OrganizationGrant numberCountry
BMBF03SF0355C Germany
EU/Energy Network project SOLAR-FP7 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)90,41520
Polymers87,6532
Non-polymers2,76218
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-201 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.530, 97.950, 125.850
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, 929 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NWN / hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron


Mass: 198.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4FeN2NiO
#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 / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
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: Dec 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 0.89→52.9 Å / Num. obs: 1167454 / % possible obs: 95.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.5
Reflection shellResolution: 0.89→0.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.1 / % possible all: 84.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9pre_1669)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUI

1wui


Resolution: 0.89→37.636 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 9.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1063 58361 5 %
Rwork0.0955 --
obs0.096 1167273 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.89→37.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 136 911 7220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146823
X-RAY DIFFRACTIONf_angle_d1.6599359
X-RAY DIFFRACTIONf_dihedral_angle_d17.2412511
X-RAY DIFFRACTIONf_chiral_restr0.1051007
X-RAY DIFFRACTIONf_plane_restr0.0121222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.90010.325716980.3232436X-RAY DIFFRACTION84
0.9001-0.91070.311816990.297732577X-RAY DIFFRACTION85
0.9107-0.92180.288817160.277232859X-RAY DIFFRACTION85
0.9218-0.93350.284317370.26533120X-RAY DIFFRACTION86
0.9335-0.94580.240217650.235833342X-RAY DIFFRACTION87
0.9458-0.95870.217417710.210333784X-RAY DIFFRACTION87
0.9587-0.97240.19818040.18634210X-RAY DIFFRACTION89
0.9724-0.98690.178318250.169234816X-RAY DIFFRACTION90
0.9869-1.00240.160918620.14935410X-RAY DIFFRACTION92
1.0024-1.01880.139419160.133136305X-RAY DIFFRACTION94
1.0188-1.03640.126419790.124937433X-RAY DIFFRACTION97
1.0364-1.05520.126420180.111838481X-RAY DIFFRACTION100
1.0552-1.07550.113720330.101838507X-RAY DIFFRACTION100
1.0755-1.09750.095120250.08738455X-RAY DIFFRACTION100
1.0975-1.12130.083620300.078238640X-RAY DIFFRACTION100
1.1213-1.14740.08420360.074238642X-RAY DIFFRACTION100
1.1474-1.17610.08320220.071838481X-RAY DIFFRACTION100
1.1761-1.20790.079920340.067738705X-RAY DIFFRACTION100
1.2079-1.24350.080220300.068138450X-RAY DIFFRACTION100
1.2435-1.28360.079120270.066138601X-RAY DIFFRACTION100
1.2836-1.32950.078820440.064538612X-RAY DIFFRACTION100
1.3295-1.38270.077720330.064238551X-RAY DIFFRACTION100
1.3827-1.44560.078220240.061938531X-RAY DIFFRACTION100
1.4456-1.52190.078720410.060638557X-RAY DIFFRACTION100
1.5219-1.61720.070820360.060138614X-RAY DIFFRACTION100
1.6172-1.74210.077220230.063938561X-RAY DIFFRACTION100
1.7421-1.91740.082120320.071238543X-RAY DIFFRACTION100
1.9174-2.19480.085320200.076538558X-RAY DIFFRACTION100
2.1948-2.76510.090820370.084338594X-RAY DIFFRACTION100
2.7651-37.66960.127920440.115538537X-RAY DIFFRACTION100

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