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Yorodumi- PDB-2bc0: Structural Analysis of Streptococcus pyogenes NADH oxidase: Wild-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bc0 | ||||||
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Title | Structural Analysis of Streptococcus pyogenes NADH oxidase: Wild-type Nox | ||||||
Components | NADH Oxidase | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / NADH oxidase / pyridine nucleotide disulfide oxidoreductase / C(4a)-peroxyflavin / conformational dynamics / cysteine oxidation / sulfinic acid | ||||||
Function / homology | Function and homology information NADH oxidase (H2O-forming) / NADH dehydrogenase (ubiquinone) activity / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Boles, W.H. / Mallett, T.C. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Structural Analysis of Streptococcus pyogenes NADH Oxidase: Conformational Dynamics Involved in Formation of the C(4a)-Peroxyflavin Intermediate. Authors: Wallen, J.R. / Mallett, T.C. / Okuno, T. / Parsonage, D. / Sakai, H. / Tsukihara, T. / Claiborne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bc0.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bc0.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/2bc0 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/2bc0 | HTTPS FTP |
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-Related structure data
Related structure data | 2bc1C 2bcpC 1joaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53492.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pTrcHis A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q1JLP2, UniProt: Q5XC60*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium sulfate, Na-K tartrate, Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→200 Å / Num. all: 69836 / Num. obs: 69836 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.39 |
Reflection shell | Resolution: 1.96→2.05 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.24 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JOA (NADH peroxidase; poly-alanine) Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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