+Open data
-Basic information
Entry | Database: PDB / ID: 1dj1 | ||||||
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Title | CRYSTAL STRUCTURE OF R48A MUTANT OF CYTOCHROME C PEROXIDASE | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / HEME ENZYME / CAVITY MUTANT | ||||||
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: 1.93 Å | ||||||
Authors | Hirst, J. / Goodin, D.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Unusual oxidative chemistry of N(omega)-hydroxyarginine and N-hydroxyguanidine catalyzed at an engineered cavity in a heme peroxidase. Authors: Hirst, J. / 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 | 1dj1.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dj1.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1dj1 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1dj1 | 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: 33139.824 Da / Num. of mol.: 1 / Mutation: R48A 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: 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: 2.62 Å3/Da / Density % sol: 53.04 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: POTASSIUM PHOSPHATE, 2-METHYL-2,4-PENTANEDIOL, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||
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: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→7.7 Å / Num. all: 23101 / Num. obs: 23101 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.92→2.04 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.199 / % possible all: 43 |
Reflection shell | *PLUS % possible obs: 43 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Resolution: 1.93→10 Å / σ(F): 4 / Stereochemistry target values: ENGH & HUBER /
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Refinement step | Cycle: LAST / Resolution: 1.93→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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