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Yorodumi- PDB-3use: Crystal Structure of E. coli hydrogenase-1 in its as-isolated form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3use | ||||||
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Title | Crystal Structure of E. coli hydrogenase-1 in its as-isolated form | ||||||
Components | (Hydrogenase-1 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / MEMBRANE-BOUND HYDROGENASE | ||||||
Function / homology | Function and homology information hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å | ||||||
Authors | Volbeda, A. / Fontecilla-Camps, J.C. / Darnault, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Authors: Volbeda, A. / Amara, P. / Darnault, C. / Mouesca, J.M. / Parkin, A. / Roessler, M.M. / Armstrong, F.A. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3use.cif.gz | 748.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3use.ent.gz | 603.9 KB | Display | PDB format |
PDBx/mmJSON format | 3use.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3use_validation.pdf.gz | 883.9 KB | Display | wwPDB validaton report |
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Full document | 3use_full_validation.pdf.gz | 892.6 KB | Display | |
Data in XML | 3use_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 3use_validation.cif.gz | 107.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/3use ftp://data.pdbj.org/pub/pdb/validation_reports/us/3use | HTTPS FTP |
-Related structure data
Related structure data | 3uqyC 3uscC 1yqwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | THE TWO DESCRIBED BIOMOLECULES 1 AND 2 ARE RELATED BY NON-CRYSTALLOGRAPHIC TWOFOLD SYMMETRY. IT IS PLAUSIBLE THAT TOGETHER THEY FORM A FUNCTIONAL TETRAMER (WHICH MAY ALSO BE DESCRIBED AS A DIMER OF HETERO-DIMERS, BIOMOLECULE 3). |
-Components
-Hydrogenase-1 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 36814.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: b0972, hyaA, JW0954 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P69739, hydrogenase (acceptor) #2: Protein | Mass: 64751.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: b0973, hyaB, JW0955 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor) |
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-Sugars , 1 types, 2 molecules
#7: Sugar |
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-Non-polymers , 12 types, 1284 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | #14: Chemical | #15: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | SF3 DESIGNATES A FE4-S3 CLUSTER IN A VERY OXIDIZED STATE WITH TOTAL CORE CHARGE OF +5 F4S ...SF3 DESIGNATES |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: PEG4000, LiSO4, DTT, DMM, pH 8.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.94645 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011 / Details: Toroidal mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.94645 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→100 Å / Num. all: 372270 / Num. obs: 194962 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.905 % / Biso Wilson estimate: 18.782 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.78 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1YQW Resolution: 1.67→29.82 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.1114 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9236 / SU B: 3.445 / SU ML: 0.051 / SU R Cruickshank DPI: 0.1138 / SU Rfree: 0.0819 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.19 Å2 / Biso mean: 13.1137 Å2 / Biso min: 4.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→29.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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