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- PDB-1cck: ALTERING SUBSTRATE SPECIFICITY OF CYTOCHROME C PEROXIDASE TOWARDS... -

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Basic information

Entry
Database: PDB / ID: 1cck
TitleALTERING SUBSTRATE SPECIFICITY OF CYTOCHROME C PEROXIDASE TOWARDS A SMALL MOLECULAR SUBSTRATE PEROXIDASE BY SUBSTITUTING TYROSINE FOR PHE 202
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / 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. / Plant heme peroxidase family profile. / Haem peroxidase ...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. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCao, Y. / Musah, R.A. / Wilcox, S.K. / Goodin, D.B. / Mcree, D.E.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of recombinant pea cytosolic ascorbate peroxidase.
Authors: Patterson, W.R. / Poulos, T.L.
#1: Journal: Biochemistry / Year: 1996
Title: Altering Substrate Specificity at the Heme Edge of Cytochrome C Peroxidase
Authors: Wilcox, S.K. / Jensen, G.M. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B.
#2: Journal: Biochemistry / Year: 1993
Title: The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the Tryptophan Free Radical to the Heme
Authors: Goodin, D.B. / Mcree, D.E.
History
DepositionJan 2, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)33,8582
Polymers33,2421
Non-polymers6161
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.500, 73.400, 44.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C PEROXIDASE / CCP/F202Y


Mass: 33241.938 Da / Num. of mol.: 1 / Mutation: F202Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Gene: CCP / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): CCP(MKT) / 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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.1 Å3/Da / Density % sol: 61 %
Crystal growMethod: dialaysis / Details: DIALYSIS AGAINST DISTILLED WATER, dialaysis
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995 / Details: NO
RadiationMonochromator: NO / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 23157 / % possible obs: 91.3 % / Observed criterion σ(I): 1.1 / Redundancy: 2.2 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.094 / Net I/σ(I): 7.1
Reflection shellResolution: 2.01→2.09 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1 / Rsym value: 0.29 / % possible all: 77.5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CCA

1cca


Resolution: 2.1→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 16716
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 43 107 3014
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19.PRO2
X-RAY DIFFRACTION2TOPH19.HIS
Refinement
*PLUS
Rfactor obs: 0.184 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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