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- PDB-2eun: Cytochrome c peroxidase (CCP) in complex with 2,4-diaminopyrimidine -

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Basic information

Entry
Database: PDB / ID: 2eun
TitleCytochrome c peroxidase (CCP) in complex with 2,4-diaminopyrimidine
Componentscytochrome c peroxidase
KeywordsOXIDOREDUCTASE / engineered ligand binding site
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Peroxidase; domain 1 / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Peroxidase; domain 1 / Plant heme peroxidase family profile. / Peroxidase / Haem peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PYRIMIDINE-2,4-DIAMINE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBrenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Probing molecular docking in a charged model binding site.
Authors: Brenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K.
History
DepositionOct 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1853
Polymers33,4581
Non-polymers7272
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.85, 73.71, 105.22
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cytochrome c peroxidase /


Mass: 33458.258 Da / Num. of mol.: 1 / Mutation: W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid: pT7 CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LG3 / PYRIMIDINE-2,4-DIAMINE / 2,4-Diaminopyrimidine


Mass: 110.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM potassium phosphate 20% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→36.85 Å / Num. obs: 38278 / % possible obs: 94.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.1
Reflection shellResolution: 1.49→1.54 Å / % possible all: 58

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36 Å
RfactorNum. reflectionSelection details
Rfree0.226 1935 random
Rwork0.193 --
all0.194 36118 -
obs0.194 34183 -
Refinement stepCycle: LAST / Resolution: 1.7→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 51 247 2645

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