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Yorodumi- PDB-1aa4: SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aa4 | ||||||
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Title | SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Musah, R.A. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity. Authors: Fitzgerald, M.M. / Musah, R.A. / McRee, D.E. / 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 | 1aa4.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aa4.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aa4_validation.pdf.gz | 747 KB | Display | wwPDB validaton report |
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Full document | 1aa4_full_validation.pdf.gz | 753.4 KB | Display | |
Data in XML | 1aa4_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1aa4_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/1aa4 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/1aa4 | HTTPS FTP |
-Related structure data
Related structure data | 1aesC 1aetC 1aeuC 1cciC 1rycC 1ccaS 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: T1M, T2K, P3T, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: BL21 / Cellular location: MITOCHONDRIA / Gene: CCP / Organelle: MITOCHONDRIA / 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: Water | ChemComp-HOH / |
Sequence details | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM 2CYP BY STRAIN-RELATED SUBSTITUTIONS OF THR 52 BY ILE AND ...THIS CYTOCHROME |
-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 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: May 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.1 Å / Num. obs: 19099 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.102 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.09→2.23 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.31 / % possible all: 35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CCA Resolution: 2.1→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.5 / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→7 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.189 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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