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Yorodumi- PDB-2icv: Kinetic and Crystallographic Studies of a Redesigned Manganese-Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2icv | ||||||
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Title | Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Manganese oxidation / metal-binding site / protein engineering / metalloprotein / biomimetic | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Pfister, T. / Mirarefi, A.Y. / Gengenbach, A.J. / Zhao, X. / Conaster, C.D.N. / Gao, Y.G. / Robinson, H. / Zukoski, C.F. / Wang, A.H.J. / Lu, Y. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2007 Title: Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase Authors: Pfister, T.D. / Mirarefi, A.Y. / Gengenbach, A.J. / Zhao, X. / Danstrom, C. / Conatser, N. / Gao, Y.-G. / Robinson, H. / Zukoski, C.F. / Wang, A.H.-J. / Lu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2icv.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2icv.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 2icv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2icv_validation.pdf.gz | 827.3 KB | Display | wwPDB validaton report |
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Full document | 2icv_full_validation.pdf.gz | 835 KB | Display | |
Data in XML | 2icv_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2icv_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/2icv ftp://data.pdbj.org/pub/pdb/validation_reports/ic/2icv | HTTPS FTP |
-Related structure data
Related structure data | 2ia8C 1besS 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: 33260.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-CO / |
#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: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.0 M hexanediol in 0.1 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 35391 / Num. obs: 34426 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.6→30 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.302 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1BES Resolution: 1.6→10 Å / σ(F): 4 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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