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- PDB-4jm6: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jm6 | ||||||
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Title | Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 2,4-diaminopyrimidine | ||||||
![]() | Cytochrome c peroxidase | ||||||
![]() | OXIDOREDUCTASE / Model system / bulk solvent / ordered waters / docking / ligand binding / free energy calculation / molecular dynamics | ||||||
Function / homology | ![]() cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / mitochondrial matrix / heme binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boyce, S.E. / Fischer, M. / Fish, I. | ||||||
![]() | ![]() Title: Blind prediction of charged ligand binding affinities in a model binding site. Authors: Rocklin, G.J. / Boyce, S.E. / Fischer, M. / Fish, I. / Mobley, D.L. / Shoichet, B.K. / Dill, K.A. #1: ![]() Title: Docking to a water-filled model binding site in Cytochrome c Peroxidase Authors: Barelier, S. / Boyce, S.E. / Fischer, M. / Fish, I. / Goodin, D.B. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.1 KB | Display | ![]() |
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PDB format | ![]() | 130.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.3 KB | Display | ![]() |
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Full document | ![]() | 817.8 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jm5C ![]() 4jm8C ![]() 4jm9C ![]() 4jmaC ![]() 4jmwC ![]() 4jplC ![]() 4jptC ![]() 4jpuC ![]() 4jqjC ![]() 4jqkC ![]() 4jqmC ![]() 4jqnC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32928.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, deletions G192-A193 / Mutation: P190G, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: RM11-1a / Gene: CCP1 CCP CPO YKR066C, SCRG_04081 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-LG3 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 283 K / pH: 6 Details: Apo crystal grown in 500mM MES, pH 6.0. Soaked into 50mM 2,4-diaminopyrimidine, 25% MPD pH 4.5 (30min-1h), temperature 283K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2009 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.45→61.66 Å / Num. obs: 72171 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.42 Å2 / Biso mean: 20.3654 Å2 / Biso min: 8.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→39.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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