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- PDB-2pcb: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS... -

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Basic information

Entry
Database: PDB / ID: 2pcb
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C
Components
  • CYTOCHROME C
  • CYTOCHROME C PEROXIDASE (CCP)
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / response to reactive oxygen species / hydrogen peroxide catabolic process / apoptotic signaling pathway / peroxidase activity ...cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / response to reactive oxygen species / hydrogen peroxide catabolic process / apoptotic signaling pathway / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / lipid binding / mitochondrion / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Cytochrome c-like domain / Peroxidase, active site ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Cytochrome c-like domain / Peroxidase, active site / Peroxidases active site signature. / Cytochrome Bc1 Complex; Chain D, domain 2 / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsPelletier, H. / Kraut, J.
Citation
Journal: Science / Year: 1992
Title: Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c.
Authors: Pelletier, H. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis
Authors: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Three Dimensional Structure of Horse Heart Cytochrome C
Authors: Bushnell, G.W. / Louie, G.V. / Brayer, G.D.
#3: Journal: J.Biol.Chem. / Year: 1987
Title: Co-Crystals of Yeast Cytochrome C Peroxidase and Horse Heart Cytochrome C
Authors: Poulos, T.L. / Sheriff, S. / Howard, A.J.
History
DepositionApr 14, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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 / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE (CCP)
B: CYTOCHROME C
C: CYTOCHROME C PEROXIDASE (CCP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1146
Polymers79,2653
Non-polymers1,8493
Water6,071337
1
A: CYTOCHROME C PEROXIDASE (CCP)
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7284
Polymers45,4952
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYTOCHROME C PEROXIDASE (CCP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3862
Polymers33,7701
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.300, 105.300, 186.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CYTOCHROME C PEROXIDASE (CCP)


Mass: 33769.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organ: HEART / References: UniProt: P00431
#2: Protein CYTOCHROME C


Mass: 11725.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / References: UniProt: P00004
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 337 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mM1dropKH2PO4
21.5 mMprotein1drop
318-22 %MPD1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 24671 / % possible obs: 93 % / Rmerge(I) obs: 0.055

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.178
Details: THE YEAST CCP USED HERE IS A RECOMBINANT (CALLED CCP(MI) AND EXPRESSED IN E. COLI) WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS ...Details: THE YEAST CCP USED HERE IS A RECOMBINANT (CALLED CCP(MI) AND EXPRESSED IN E. COLI) WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS STRUCTURE DUE TO DISORDER. AFTER FINAL REFINEMENT THERE WAS ADDITIONAL ELECTRON DENSITY FOUND IN THE ASYMMETRIC UNIT WHICH HAS BEEN ATTRIBUTED TO A PARTIALLY OCCUPIED SECOND CYTOCHROME C MOLECULE. THE COORDINATES FOR A POSSIBLE SECOND CYTOCHROME C SITE HAVE NOT BEEN INCLUDED IN THIS ENTRY. SEE REFERENCE 1 FOR DETAILS.
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 129 337 6031
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_d2.7

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