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Yorodumi- PDB-2aqd: cytochrome c peroxidase (CCP) in complex with 2,5-diaminopyridine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aqd | ||||||
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Title | cytochrome c peroxidase (CCP) in complex with 2,5-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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 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 | 2aqd.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aqd.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 2aqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/2aqd ftp://data.pdbj.org/pub/pdb/validation_reports/aq/2aqd | HTTPS FTP |
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-Related structure data
Related structure data | 2anzC 2as1C 2as2C 2as3C 2as4C 2as6C 2eunC 2euoC 2eupC 2euqC 2eurC 2eusC 2eutC 2euuC 1ac4S C: citing same article (ref.) S: Starting model for refinement |
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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 / Fragment: cytochrome c peroxidase / 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-DA1 / |
#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: 3.07 Å3/Da / Density % sol: 59.62 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03313 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03313 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 90551 / Num. obs: 88088 / % possible obs: 99.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.35→1.4 Å / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1AC4 Resolution: 1.35→10 Å / Num. parameters: 24630 / Num. restraintsaints: 29706 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4 %
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2735 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
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Refine LS restraints |
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