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Yorodumi- PDB-1krj: Engineering Calcium-binding site into Cytochrome c Peroxidase (CcP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1krj | ||||||
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Title | Engineering Calcium-binding site into Cytochrome c Peroxidase (CcP) | ||||||
Components | Cytochrome c Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Cation-binding loop / Calcium selectivity / Trp191 cationic-radical / open/closed conformer / bidentate bond / pentagonal bipyrimidal geometry / lignin peroxidase | ||||||
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 Å | ||||||
Authors | Bonagura, C.A. / Bhaskar, B. / Sundaramoorthy, M. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Conversion of an engineered potassium-binding site into a calcium-selective site in cytochrome c peroxidase. Authors: Bonagura, C.A. / Bhaskar, B. / Sundaramoorthy, M. / Poulos, T.L. | ||||||
History |
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Remark 400 | COMPOUND Largely a helical bundle protein containing a distinct distal and proximal heme domains. ...COMPOUND Largely a helical bundle protein containing a distinct distal and proximal heme domains. Proximal heme domain contains the cation-binding loop which in the present case contains Calcium coordinated by the residues 190-199 of the loop. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1krj.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1krj.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 1krj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1krj_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 1krj_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 1krj_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1krj_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1krj ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1krj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Largely a helical bundle protein containing a distinct distal and proximal heme domains. Proximal heme domian contains the cation-binding loop which in the present case contains Calcium coordinated by the residues 190-199 of the loop |
-Components
#1: Protein | Mass: 33661.277 Da / Num. of mol.: 1 / Fragment: Proximal Cation-binding Loop / Mutation: A176T, G192D, A194T, T199D, E201S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OPBYC / Plasmid: pT7CcP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-HEM / |
#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: 3.06 Å3/Da / Density % sol: 59.85 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2-Methyl-2,4-Pentanediol (MPD), potassium phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 29, 1998 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 28764 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8627 % / Rmerge(I) obs: 0.082 / Rsym value: 0.057 / Net I/σ(I): 19.2082 |
Reflection shell | Resolution: 2→2.02 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3023 / Num. unique all: 706 / Rsym value: 0.354 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 28701 / % possible obs: 99.8 % / Num. measured all: 155672 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Potassium-binding CcP (CcPK2) Resolution: 2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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