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- PDB-2cyp: Crystal structure of yeast cytochrome C peroxidase refined at 1.7... -

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Basic information

Entry
Database: PDB / ID: 2cyp
TitleCrystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE (H2O2(A))
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 / Resolution: 1.7 Å
AuthorsFinzel, B.C. / Poulos, T.L. / Kraut, J.
Citation
Journal: J.Biol.Chem. / Year: 1984
Title: Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
#1: Journal: Pept.Protein Rev. / Year: 1984
Title: Heme Enzyme Structure and Function
Authors: Poulos, T.L. / Finzel, B.C.
#2: Journal: J.Biol.Chem. / Year: 1980
Title: A Hypothetical Model of the Cytochrome C Peroxidase-Cytochrome C Electron Transfer Complex
Authors: Poulos, T.L. / Kraut, J.
#3: Journal: J.Biol.Chem. / Year: 1980
Title: The Stereochemistry of Peroxidase Catalysis
Authors: Poulos, T.L. / Kraut, J.
#4: Journal: J.Biol.Chem. / Year: 1980
Title: The Crystal Structure of Cytochrome C Peroxidase
Authors: Poulos, T.L. / Freer, S.T. / Alden, R.A. / Edwards, S.L. / Skogland, U. / Takio, K. / Eriksson, B. / Xuong, N.-H. / Yonetani, T. / Kraut, J.
#5: Journal: J.Biol.Chem. / Year: 1978
Title: Crystallographic Determination of the Heme Orientation and Location of the Cyanide Binding Site in Yeast Cytochrome C Peroxidase
Authors: Poulos, T.L. / Freer, S.T. / Alden, R.A. / Xuong, N.H. / Edwards, S.L. / Hamlin, R.C. / Kraut, J.
History
DepositionAug 27, 1985Processing site: BNL
SupersessionJan 21, 1986ID: 1CYP
Revision 1.0Jan 21, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)34,2043
Polymers33,5711
Non-polymers6322
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Atom site foot note1: THIS ATOM WAS DESIGNATED HOH 595 BY THE DEPOSITORS. / 2: SEE REMARK 4.

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Components

#1: Protein CYTOCHROME C PEROXIDASE


Mass: 33571.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(v/v)MPD11
250 mMpotassium phosphate11

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 44888 / Num. measured all: 181721 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.202 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 44 262 2609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Num. reflection obs: 44888 / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal target: 0.03

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