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- PDB-3m2e: Crystallographic and Single Crystal Spectral Analysis of the Pero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m2e | ||||||
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Title | Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate | ||||||
![]() | Cytochrome c peroxidase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / Cytochrome c peroxidase (CCP) / Heme / Hydrogen peroxide / Iron / Metal-binding / Mitochondrion / Organic radical / Peroxidase | ||||||
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 | ![]() ![]() | ||||||
![]() | Meharenna, Y.T. / Poulos, T.L. | ||||||
![]() | ![]() Title: Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Authors: Meharenna, Y.T. / Doukov, T. / Li, H. / Soltis, S.M. / Poulos, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.5 KB | Display | ![]() |
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PDB format | ![]() | 127.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.5 KB | Display | ![]() |
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Full document | ![]() | 760.8 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m23C ![]() 3m25C ![]() 3m26C ![]() 3m27C ![]() 3m28C ![]() 3m29C ![]() 3m2aC ![]() 3m2bC ![]() 3m2cC ![]() 3m2dC ![]() 3m2fC ![]() 3m2gC ![]() 3m2hC ![]() 3m2iC 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: 33315.012 Da / Num. of mol.: 1 / Fragment: UNP residues 71-361 / Mutation: N184R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CCP, CCP1, CPO, YKR066C / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 60.67 % |
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Crystal grow | Temperature: 277.2 K / pH: 6 Details: 10uL (350-400uM protein), 22% MPD, 50mM tris phoshate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K |
-Data collection
Diffraction | Mean temperature: 65 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 77965 / % possible obs: 95.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.522 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.4→50 Å / Num. parameters: 36595 / Num. restraintsaints: 33104 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2206.94 / Occupancy sum non hydrogen: 2964 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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Refine LS restraints |
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