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Yorodumi- PDB-1dso: CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX AT PH 6, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dso | ||||||
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Title | CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX AT PH 6, ROOM TEMPERATURE. | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / HEME ENZYME / PEROXIDASE / CAVITY MUTANT / LIGAND BINDING | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / 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 / SYNCHROTRON / Resolution: 2.03 Å | ||||||
Authors | Hirst, J. / Wilcox, S.K. / Williams, P.A. / McRee, D.E. / Goodin, D.B. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 1. Effects on structure. Authors: Hirst, J. / Wilcox, S.K. / Williams, P.A. / Blankenship, J. / McRee, D.E. / Goodin, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dso.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dso.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dso_validation.pdf.gz | 480.5 KB | Display | wwPDB validaton report |
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Full document | 1dso_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | 1dso_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1dso_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1dso ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1dso | HTTPS FTP |
-Related 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: 33245.945 Da / Num. of mol.: 1 / Mutation: H175G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PT7CCP / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-IMD / |
#4: 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: 3.2 Å3/Da / Density % sol: 61.56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: microdialysis / pH: 6 Details: MES, imidazole, pH 6, MICRODIALYSIS, temperature 288K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 281 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→9.08 Å / Num. all: 26702 / Num. obs: 26702 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.726 / % possible all: 66.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / % possible obs: 97 % / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Resolution: 2.03→9.1 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.03→9.1 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 9.1 Å / σ(F): 4 / Rfactor obs: 0.17 / Rfactor Rwork: 0.172 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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