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Yorodumi- PDB-1aef: SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aef | ||||||
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Title | SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (3-AMINOPYRIDINE) | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / TRANSIT PEPTIDE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Musah, R.A. / Jensen, G.M. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. Authors: Musah, R.A. / Jensen, G.M. / Bunte, S.W. / Rosenfeld, R.J. / 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 | 1aef.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aef.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/1aef ftp://data.pdbj.org/pub/pdb/validation_reports/ae/1aef | HTTPS FTP |
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-Related structure data
Related structure data | 1aebC 1aedC 1aeeC 1aegC 1aehC 1aejC 1aekC 1aemC 1aenC 1aeoC 1aeqC 1aa4S 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 Details: CRYSTAL FORM BY Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: BL21 / Cellular location: MITOCHONDRIAMitochondrion / Gene: CCP / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PT7CCP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): CCP (MKT) / 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-3AP / |
#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: 3.2 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||
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Crystal grow | pH: 6 Details: 20% MPD, 40 MM PHOSPHATE PH 6.0. A SINGLE CRYSTAL OF W191G WAS SOAKED IN 50MM 3-AMINOPYRIDINE IN 40% MPD AND 60 MM PHOSPHATE AT PH 4.5. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. obs: 23265 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.087 / Net I/σ(I): 11.94 |
Reflection shell | Resolution: 2.03→2.18 Å / Redundancy: 1.68 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.51 / Rsym value: 0.54 / % possible all: 79 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AA4 Resolution: 2.1→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.5 / σ(F): 0 Details: THE PROTEIN AND WATER COORDINATES WERE TAKEN FROM PDB ENTRY 1AA4. THE LIGAND COORDINATES WERE MEASURED FROM THE OMIT MAP. NO REFINEMENT WAS CARRIED OUT ON THE RESULTING SET OF COORDINATES, ...Details: THE PROTEIN AND WATER COORDINATES WERE TAKEN FROM PDB ENTRY 1AA4. THE LIGAND COORDINATES WERE MEASURED FROM THE OMIT MAP. NO REFINEMENT WAS CARRIED OUT ON THE RESULTING SET OF COORDINATES, WHICH ARE THE COORDINATES PRESENTED IN THIS ENTRY.
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Refinement step | Cycle: LAST / Resolution: 2.1→7 Å
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