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Basic information

Entry
Database: PDB / ID: 1ebe
TitleLaue diffraction study on the structure of cytochrome c peroxidase compound I
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (H2O2(A)) / COMPOUND I / LAUE DIFFRACTION
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 / OXYGEN ATOM / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsFulop, V. / Phizackerley, R.P. / Soltis, S.M. / Clifton, I.J. / Wakatsuki, S. / Erman, J.E. / Hajdu, J. / Edwards, S.L.
Citation
Journal: Structure / Year: 1994
Title: Laue Diffraction Study on the Structure of Cytochrome C Peroxidase Compound I
Authors: Fulop, V. / Phizackerley, R.P. / Soltis, S.M. / Clifton, I.J. / Wakatsuki, S. / Erman, J.E. / Hajdu, J. / Edwards, S.L.
#1: Journal: J.Biol.Chem. / Year: 1984
Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
History
DepositionJul 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Data collection
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2053
Polymers33,5721
Non-polymers6322
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.400, 76.800, 51.400
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


Mass: 33572.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPOUND I / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / 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: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREMOVES TOXIC RADICALS THAT ARE PRODUCED WITHIN CELLS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growpH: 6
Details: SEE REFERENCE EDWARDS ET AL. BIOCHEMISTRY 26, 1503-1511 (1987), pH 6.00
Crystal grow
*PLUS
Method: other / Details: Edwards, S.L., (1987) Biochemistry, 26, 1503.

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Type: CHESS / Wavelength: 0.2-2.5
DetectorType: KODAK DEF5 / Detector: FILM / Date: Nov 15, 1990
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.21
22.51
ReflectionResolution: 2.2→8 Å / Num. obs: 9089 / % possible obs: 42 % / Observed criterion σ(I): -2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 37.5
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 30274 / Num. measured all: 94847 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
LEAPdata reduction
LEAPdata scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2CYP

2cyp


Resolution: 2.2→8 Å / σ(F): 2
Details: OMITTED FROM THIS ENTRY ARE DISORDERED SURFACE ATOMS WHOSE POSITION COULD NOT BE DETERMINED EVEN AFTER REFINEMENT. ALL ATOMS PRESENT IN ENTRY 2CYP WERE USED IN REFINEMENT
RfactorNum. reflection% reflection
Rwork0.144 --
obs0.144 9070 42 %
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 44 261 2603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24

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