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Yorodumi- PDB-1dsg: CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX AT PH 5, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dsg | ||||||
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Title | CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX AT PH 5, 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: 2.56 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 | 1dsg.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dsg.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1dsg ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1dsg | HTTPS FTP |
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-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: 61.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: microdialysis / pH: 5.2 Details: MES, imidazole, pH 5.2, MICRODIALYSIS, temperature 288K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||
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: 2.56→11.4 Å / Num. all: 13358 / Num. obs: 13358 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.223 / Net I/σ(I): 1.7 |
Reflection shell | Resolution: 2.56→2.62 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.637 / % possible all: 31.7 |
Reflection | *PLUS Highest resolution: 3.2 Å / % possible obs: 96.3 % / Rmerge(I) obs: 0.16 |
Reflection shell | *PLUS Mean I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Resolution: 2.56→11 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.56→11 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Lowest resolution: 11 Å / σ(F): 4 / Rfactor obs: 0.16 / Rfactor Rwork: 0.157 / Highest resolution: 3.2 Å | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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