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Yorodumi- PDB-1cmu: THE ROLE OF ASPARTATE-235 IN THE BINDING OF CATIONS TO AN ARTIFIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cmu | ||||||
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Title | THE ROLE OF ASPARTATE-235 IN THE BINDING OF CATIONS TO AN ARTIFICIAL CAVITY AT THE RADICAL SITE OF CYTOCHROME C PEROXIDASE | ||||||
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 | Fitzgerald, M.M. / Trester, M.L. / Jensen, G.M. / Mcree, D.E. / Goodin, D.B. | ||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase. Authors: Fitzgerald, M.M. / Trester, M.L. / Jensen, G.M. / McRee, D.E. / Goodin, D.B. #1: Journal: Biochemistry / Year: 1994 Title: Small Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome C Peroxidase Authors: Fitzgerald, M.M. / Churchill, M.J. / Mcree, D.E. / Goodin, D.B. #2: 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 | 1cmu.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cmu.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cmu ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cmu | 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: 33457.270 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.59 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: Wang, J.M., (1990) Biochemistry, 29, 7160. | ||||||||||||||||||||
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: 17426 / % possible obs: 83 % / Observed criterion σ(I): 9.3 / Num. measured all: 48753 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Mean I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Resolution: 2.1→5 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.195 / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.9 |