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Yorodumi- PDB-1dse: CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX, WITH PHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dse | ||||||
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Title | CYTOCHROME C PEROXIDASE H175G MUTANT, IMIDAZOLE COMPLEX, WITH PHOSPHATE BOUND, PH 6, 100K | ||||||
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 / Resolution: 2 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 | 1dse.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dse.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dse_validation.pdf.gz | 488.7 KB | Display | wwPDB validaton report |
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Full document | 1dse_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | 1dse_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1dse_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1dse ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1dse | 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: 33244.961 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-PO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-IMD / |
#5: 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: 3.04 Å3/Da / Density % sol: 59.48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 6 Details: phosphate, imidazole, pH 6, MICRODIALYSIS, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19 Å / Num. all: 38609 / Num. obs: 38609 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.189 / % possible all: 91.1 |
Reflection | *PLUS |
Reflection shell | *PLUS Mean I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Resolution: 2→19 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→19 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 19 Å / σ(F): 4 / Rfactor Rwork: 0.196 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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