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Yorodumi- PDB-1sbm: Crystal Structure of Reduced Mesopone cytochrome c peroxidase (R-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sbm | ||||||
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Title | Crystal Structure of Reduced Mesopone cytochrome c peroxidase (R-isomer) | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Bifunctional catalyst / Proximal loop / Trp191 radical / 4-mesoporphyrin / nitrite reductase | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Bhaskar, B. / Immoos, C.E. / Sulc, F. / Cohen, M.S. / Farmer, P.J. / Poulos, T.L. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Resting (Fe3+), Reduced (Fe2+) and Reduced-NO adduct of Mesopone cytochrome c peroxidase (MpCcP) - R-isomer Authors: Bhaskar, B. / Immoos, C.E. / Sulc, F. / Cohen, M.S. / Farmer, P.J. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sbm.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sbm.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/1sbm ftp://data.pdbj.org/pub/pdb/validation_reports/sb/1sbm | HTTPS FTP |
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-Related structure data
Related structure data | 1s73S 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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Unit cell |
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Details | Helical bundle protein present in intermembrane space of Baker's yeast. Protein is divided into 2 distinct distal and proximal heme domians. Protein belongs to P212121 space group with one molecule in the asymmetric unit |
-Components
#1: Protein | Mass: 33571.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-FMI / |
#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: 3.07 Å3/Da / Density % sol: 59.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2-methyl-2,4-pentanediol (MPD), 100mM potassium phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2003 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. obs: 47110 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.32 % / Rmerge(I) obs: 0.062 / Rsym value: 0.043 / Net I/σ(I): 20.98 |
Reflection shell | Resolution: 1.69→1.72 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2236 / Rsym value: 0.534 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1S73 Resolution: 1.69→1.72 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.69→1.72 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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