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Yorodumi- PDB-2zcu: Crystal structure of a new type of NADPH-dependent quinone oxidor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zcu | ||||||
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Title | Crystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from escherichia coli | ||||||
Components | Uncharacterized oxidoreductase ytfG | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA SANDWICH | ||||||
Function / homology | Function and homology information NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Kim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from Escherichia coli Authors: Kim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zcu.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zcu.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zcu_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 2zcu_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 2zcu_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 2zcu_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/2zcu ftp://data.pdbj.org/pub/pdb/validation_reports/zc/2zcu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29762.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: strain K12 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39315, NADPH:quinone reductase |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 285 K / Method: evaporation / pH: 7.5 Details: PEG 4000, COPPER CHLRORIDE, AMMONIUM SULFATE, HEPES, pH 7.50, EVAPORATION, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97934, 0.97947, 0.97167, 1.12714 | |||||||||||||||
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: May 10, 2003 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. obs: 28204 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.062 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Rsym value: 0.294 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 435259.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 98.99 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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