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Yorodumi- PDB-2euu: Cytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol -
+Open data
-Basic information
Entry | Database: PDB / ID: 2euu | ||||||
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Title | Cytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol | ||||||
Components | cytochrome c peroxidase | ||||||
Keywords | OXIDOREDUCTASE / engineered ligand binding site | ||||||
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: 1.45 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 | 2euu.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2euu.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 2euu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2euu_validation.pdf.gz | 805.9 KB | Display | wwPDB validaton report |
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Full document | 2euu_full_validation.pdf.gz | 806.7 KB | Display | |
Data in XML | 2euu_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2euu_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/2euu ftp://data.pdbj.org/pub/pdb/validation_reports/eu/2euu | HTTPS FTP |
-Related structure data
Related structure data | 2anzC 2aqdC 2as1C 2as2C 2as3C 2as4C 2as6C 2eunC 2euoC 2eupC 2euqC 2eurC 2eusC 2eutC 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-BVG / |
#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: 2.51 Å3/Da / Density % sol: 51 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 |
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 | Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 59787 / Num. obs: 59787 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.456 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1AEE Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.905 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20 /
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