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Yorodumi- PDB-1ccg: CONSTRUCTION OF A BIS-AQUO HEME ENZYME AND REPLACEMENT WITH EXOGE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ccg | ||||||
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Title | CONSTRUCTION OF A BIS-AQUO HEME ENZYME AND REPLACEMENT WITH EXOGENOUS LIGAND | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE(H2O2(A)) | ||||||
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: 2.1 Å | ||||||
Authors | Mcree, D.E. / Jensen, G.M. / Fitzgerald, M.M. / Siegel, H.A. / Goodin, D.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Construction of a bisaquo heme enzyme and binding by exogenous ligands. Authors: McRee, D.E. / Jensen, G.M. / Fitzgerald, M.M. / Siegel, H.A. / Goodin, D.B. #1: Journal: Biochemistry / Year: 1993 Title: The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure and Coupling of the Tryptophan Free-Radical to the Heme Authors: Goodin, D.B. / Mcree, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ccg.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ccg.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ccg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ccg_validation.pdf.gz | 480.1 KB | Display | wwPDB validaton report |
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Full document | 1ccg_full_validation.pdf.gz | 488.9 KB | Display | |
Data in XML | 1ccg_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1ccg_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1ccg ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1ccg | 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: 33144.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) 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 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 K / pH: 6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 18373 / % possible obs: 94 % / Num. measured all: 86150 / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Resolution: 2.1→5 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |