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Yorodumi- PDB-1ac4: VARIATION IN THE STRENGTH OF A CH TO O HYDROGEN BOND IN AN ARTIFI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ac4 | ||||||
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Title | VARIATION IN THE STRENGTH OF A CH TO O HYDROGEN BOND IN AN ARTIFICIAL PROTEIN CAVITY (2,3,4-TRIMETHYL-1,3-THIAZOLE) | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / TRANSIT PEPTIDE | ||||||
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. / Jensen, G.M. / Bunte, S.W. / Rosenfeld, R. / Mcree, D.E. / Goodin, D.B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1997 Title: Variation in strength of an unconventional C-H to O hydrogen bond in an engineered 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 | 1ac4.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ac4.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ac4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ac4_validation.pdf.gz | 745.4 KB | Display | wwPDB validaton report |
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Full document | 1ac4_full_validation.pdf.gz | 751 KB | Display | |
Data in XML | 1ac4_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1ac4_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/1ac4 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/1ac4 | HTTPS FTP |
-Related structure data
Related structure data | 1cmqS 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: 33459.242 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Details: CRYSTAL FORM MKT Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: BL21 / 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: Chemical | ChemComp-TMT / |
#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 2,3,4-TRIMETHYLTHIAZOLE IN 40% MPD AND 60 MM PHOSPHATE AT PH 4.5. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: Wang, J.M. (1990) Biochemistry, 29, 7160. | |||||||||||||||||||||||||
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: 19477 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.048 / Net I/σ(I): 18.16 |
Reflection shell | Resolution: 2.03→2.19 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.24 / % possible all: 58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CMQ 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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