[English] 日本語
Yorodumi- PDB-2ycg: Structure of unreduced ferric cytochrome c peroxidase obtained by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ycg | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of unreduced ferric cytochrome c peroxidase obtained by multicrystal method | ||||||
Components | CYTOCHROME C PEROXIDASE, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / FERRIC HEME / PHOTOREDUCTION | ||||||
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: 1.81 Å | ||||||
Authors | Gumiero, A. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: To be Published Title: Hydrogen Bonds in Ferric Cytochrome C Peroxidase: A Combined X-Ray and Neutron Study Authors: Gumiero, A. / Blakeley, M.P. / Metcalfe, C.L. / Murphy, E.J. / Raven, E.L. / Moody, P.C.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ycg.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ycg.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ycg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ycg_validation.pdf.gz | 813.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ycg_full_validation.pdf.gz | 821.5 KB | Display | |
Data in XML | 2ycg_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 2ycg_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2ycg ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2ycg | HTTPS FTP |
-Related structure data
Related structure data | 2xilS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33571.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PLEICS-03 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P00431, cytochrome-c peroxidase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 1-67 IN THE UNIPROT SEQUENCE ARE A MITOCHONDR | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
---|
-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC SATURN 944+ / Detector: CCD / Date: Oct 20, 2010 / Details: VARIMAX HF OPTICS (75 MICROMETER FOCUS, 1.2KW) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→12.38 Å / Num. obs: 35815 / % possible obs: 92.24 % / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.81→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 9.6 / % possible all: 87.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XIL Resolution: 1.81→10 Å / Num. parameters: 12115 / Num. restraintsaints: 10089 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: BULK SOLVENT METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3010 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|