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- PDB-2rby: 1-methyl-5-imidazolecarboxaldehyde in complex with Cytochrome C P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rby | ||||||
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Title | 1-methyl-5-imidazolecarboxaldehyde in complex with Cytochrome C Peroxidase W191G | ||||||
![]() | Cytochrome C Peroxidase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding ...cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Graves, A.P. / Boyce, S.E. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / 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 | ![]() | 150.8 KB | Display | ![]() |
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PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.9 KB | Display | ![]() |
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Full document | ![]() | 809.2 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rayC ![]() 2razC ![]() 2rb0C ![]() 2rb1C ![]() 2rb2C ![]() 2rbnC ![]() 2rboC ![]() 2rbpC ![]() 2rbqC ![]() 2rbrC ![]() 2rbsC ![]() 2rbtC ![]() 2rbuC ![]() 2rbvC ![]() 2rbwC ![]() 2rbxC ![]() 2rbzC ![]() 2rc0C ![]() 2rc1C ![]() 2rc2C ![]() 1ac4S 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: 33198.867 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: YJM789 / Gene: ccp1, ccp, cpo / Plasmid: PT7CCP / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: A7A026, UniProt: P00431*PLUS, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-280 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % |
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Crystal grow | Temperature: 291 K / pH: 6 Details: MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 / Details: KOHZU: DOUBLE CRYSTAL SI(111) |
Radiation | Monochromator: KHOZU DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 66916 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.221 / % possible all: 99.8 |
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Processing
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Refinement | Starting model: 1AC4 Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.613 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.054 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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