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Yorodumi- PDB-2euq: Cytochrome c peroxydase (CCP) in complex with 3-thienylmethylamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2euq | ||||||
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Title | Cytochrome c peroxydase (CCP) in complex with 3-thienylmethylamine | ||||||
Components | cytochrome c peroxidase | ||||||
Keywords | OXIDOREDUCTASE / engineered ligand binding site | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / 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: 1.3 Å | ||||||
Authors | Brenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Probing molecular docking in a charged model binding site. Authors: Brenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2euq.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2euq.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2euq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/2euq ftp://data.pdbj.org/pub/pdb/validation_reports/eu/2euq | HTTPS FTP |
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-Related structure data
Related structure data | 2anzC 2aqdC 2as1C 2as2C 2as3C 2as4C 2as6C 2eunC 2euoC 2eupC 2eurC 2eusC 2eutC 2euuC 1aeeS 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: 33458.258 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pT7 CCP / 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-HEM / |
#3: Chemical | ChemComp-BVC / |
#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: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM KPi 20% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 80407 / Num. obs: 80407 / % possible obs: 95.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.297 / % possible all: 74.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1AEE Resolution: 1.3→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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