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Yorodumi- PDB-2x08: cytochrome c peroxidase: ascorbate bound to the engineered ascorb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x08 | ||||||
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Title | cytochrome c peroxidase: ascorbate bound to the engineered ascorbate binding site | ||||||
Components | CYTOCHROME C PEROXIDASE, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / METAL-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 / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Murphy, E.J. / Metcalfe, C.L. / Gumiero, A. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Engineering the substrate specificity and reactivity of a heme protein: creation of an ascorbate binding site in cytochrome c peroxidase. Authors: Murphy, E.J. / Metcalfe, C.L. / Basran, J. / Moody, P.C. / Raven, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x08.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x08.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x08_validation.pdf.gz | 780.5 KB | Display | wwPDB validaton report |
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Full document | 2x08_full_validation.pdf.gz | 784.6 KB | Display | |
Data in XML | 2x08_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2x08_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/2x08 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x08 | HTTPS FTP |
-Related structure data
Related structure data | 2x07C 2v23S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 33410.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 69-361 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Sugar | ChemComp-ASC / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 103 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 251 TO ARG ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.38 % / Description: NONE |
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Crystal grow | pH: 6 Details: DIALYSIS AGAINST PHOSPHATE BUFFER 50 MM PH 6, MPD 30% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 |
Detector | Type: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Jan 10, 2008 / Details: XENOCS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.48 Å / Num. obs: 25406 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.7 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V23 Resolution: 2.01→41.92 Å / Cor.coef. Fo:Fc: 0.938 / SU B: 2.926 / SU ML: 0.084 / ESU R: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→41.92 Å
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