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Yorodumi- PDB-4jb4: Expression, Purification, Characterization, and Solution NMR Stud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jb4 | ||||||
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Title | Expression, Purification, Characterization, and Solution NMR Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome c Peroxidase | ||||||
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: 2.39 Å | ||||||
Authors | Wohlkonig, A.C. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Expression, purification, characterization, and solution nuclear magnetic resonance study of highly deuterated yeast cytochrome C peroxidase with enhanced solubility. Authors: Volkov, A.N. / Wohlkonig, A. / Soror, S.H. / van Nuland, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jb4.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jb4.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/4jb4 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jb4 | HTTPS FTP |
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-Related structure data
Related structure data | 1zbyS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34462.270 Da / Num. of mol.: 2 / Fragment: cytochrome-c peroxidase, UNP residues 68-361 / Mutation: T1M, T2K, P3T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M NH4Cl, 0.1 M CH3COONa pH5.0 and 20% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. all: 91760 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.158 |
Reflection shell | Resolution: 2.39→2.45 Å / % possible all: 90.17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZBY Resolution: 2.39→43.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.926 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.502 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→43.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.44 Å / Num. reflection Rfree: 79 / Num. reflection Rwork: 1655 / Num. reflection obs: 1655 / Total num. of bins used: 20 |