+Open data
-Basic information
Entry | Database: PDB / ID: 2anz | ||||||
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Title | cytochrome c peroxidase in complex with 2,6-diaminopyridine | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / MODEL 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 / FOURIER SYNTHESIS / Resolution: 1.75 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 | 2anz.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2anz.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 2anz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2anz_validation.pdf.gz | 815.4 KB | Display | wwPDB validaton report |
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Full document | 2anz_full_validation.pdf.gz | 816 KB | Display | |
Data in XML | 2anz_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2anz_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/2anz ftp://data.pdbj.org/pub/pdb/validation_reports/an/2anz | HTTPS FTP |
-Related structure data
Related structure data | 2aqdC 2as1C 2as2C 2as3C 2as4C 2as6C 2eunC 2euoC 2eupC 2euqC 2eurC 2eusC 2eutC 2euuC 1ac4S 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: 33459.242 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO / Plasmid: PT7CCP / 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-26D / |
#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: 3.1 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 24, 2005 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 41392 / Num. obs: 39610 / % possible obs: 96.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1AC4 Resolution: 1.75→39.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 262020.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.9998 Å2 / ksol: 0.381305 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→39.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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