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- PDB-1ml2: Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ml2 | ||||||
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Title | Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX) | ||||||
![]() | Cytochrome c Peroxidase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome c peroxidase / ZnCcP / Zn-Protoporphyrin IX / oxygen radical / Trp cation radical / Trp-Tyr Covalent Cross-link | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bhaskar, B. / Immoos, C.E. / Shimizu, H. / Farmer, P.J. / Poulos, T.L. | ||||||
![]() | ![]() Title: A Novel Heme and Peroxide-Dependent Tryptophan-Tyrosine Cross-Link in a Mutant of Cytochrome c Peroxidase Authors: Bhaskar, B. / Immoos, C.E. / Shimizu, H. / Sulc, F. / Farmer, P.J. / Poulos, T.L. | ||||||
History |
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Remark 400 | COMPOUND ZN(II)-PROTOPORPHYRIN IX INCORPORATED INTO H52Y MUTANT OF CCP. IN THE PRESENCE OF REDOX ...COMPOUND ZN(II)-PROTOPORPHYRIN IX INCORPORATED INTO H52Y MUTANT OF CCP. IN THE PRESENCE OF REDOX INACTIVE ZN-PORPHRIN NO TRP-TYR COVALENT CROSS-LINK. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.2 KB | Display | ![]() |
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Full document | ![]() | 472.3 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mk8SC ![]() 1mkqC ![]() 1mkrC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33596.266 Da / Num. of mol.: 1 / Mutation: H52Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: OPBYC / Plasmid: pT7CcP / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2-Methyl-2,4-Pentanediol (MPD), tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 24, 2001 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 34532 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.74 % / Rmerge(I) obs: 0.044 / Rsym value: 0.051 / Net I/σ(I): 44.47 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 11.36 / Num. unique all: 1614 / Rsym value: 0.121 / % possible all: 86.8 |
Reflection | *PLUS % possible obs: 91.2 % / Num. measured all: 434384 |
Reflection shell | *PLUS % possible obs: 86.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry : 1MK8 - H52Y1 Structure Resolution: 1.65→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.5538 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS % reflection Rfree: 4.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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