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

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Basic information

Entry
Database: PDB / ID: 2pcc
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C
Components
  • CYTOCHROME C PEROXIDASE
  • ISO-1-CYTOCHROME C
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / peroxidase activity ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
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 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...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 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / 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 isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C
Authors: Louie, G.V. / Brayer, G.D.
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE
B: ISO-1-CYTOCHROME C
C: CYTOCHROME C PEROXIDASE
D: ISO-1-CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,34510
Polymers91,6874
Non-polymers2,6586
Water9,062503
1
A: CYTOCHROME C PEROXIDASE
B: ISO-1-CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1725
Polymers45,8432
Non-polymers1,3293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYTOCHROME C PEROXIDASE
D: ISO-1-CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1725
Polymers45,8432
Non-polymers1,3293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.400, 118.600, 45.100
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCHAINS LABELED A (CCP NUMBER 1) AND B (CYTOCHROME C NUMBER 1) REPRESENT ONE COMPLEX MOLECULE IN THE ASYMMETRIC UNIT, AND, LIKEWISE, CHAINS LABELED C (CCP NUMBER 2) AND D (CYTOCHROME C NUMBER 2) REPRESENT THE SECOND COMPLEX MOLECULE IN THE ASYMMETRIC UNIT. WATER MOLECULES NUMBERED 301 TO 554 ARE ASSOCIATED WITH THE FIRST COMPLEX, AND WATER MOLECULES NUMBERED 600 TO 848 ARE ASSOCIATED WITH THE SECOND COMPLEX.

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Components

#1: Protein CYTOCHROME C PEROXIDASE /


Mass: 33769.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00431
#2: Protein ISO-1-CYTOCHROME C


Mass: 12073.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00044
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN ACCORDANCE WITH THE SEQUENCE NUMBERING FOR EUKARYOTIC CYTOCHROMES C, THE SEQUENCE NUMBERING FOR ...IN ACCORDANCE WITH THE SEQUENCE NUMBERING FOR EUKARYOTIC CYTOCHROMES C, THE SEQUENCE NUMBERING FOR THE YEAST CYTOCHROMES C IN THIS STRUCTURE BEGINS WITH -5. THERE IS NO RESIDUE WITH A SEQUENCE NUMBER 0. COORDINATES FOR THE METHYL GROUPS OF THE TRIMETHYLATED LYSINE (RESIDUE 72) ARE INCLUDED IN THE 1YCC ENTRY, BUT THEY ARE NOT INCLUDED HERE DUE TO SIDE CHAIN DISORDER. RESIDUE NUMBER 72 OF THE TWO YEAST ISO-1-CYTOCHROMES C IN THIS STRUCTURE ARE LEFT AS LYSINES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropKH2PO4
240 mMdithiothreitol1drop
31 mMprotein complex1drop
4150 mM1reservoirNaCl
512-15 %PEG33501reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 37845 / % possible obs: 93 % / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / Rfactor Rwork: 0.167
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. THERE WAS UNEXPLAINED ELECTRON DENSITY ABOVE THE HEME IRON INTO WHICH WATER MOLECULES ALONE COULD NOT BE MODELED. AN SO- GROUP, A POSSIBLE DEGRADATION PRODUCT OF DTT, WAS PLACED HERE AND WAS TREATED AS AN INCOMPLETE SULFATE ION DURING REFINEMENT. THIS IS NOT A SULFATE ION. IT IS ONLY CALLED A SULFATE ION FOR SIMPLICITY.
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 176 503 7115
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.021
X-RAY DIFFRACTIONo_angle_deg2.3

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