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- PDB-3cyt: REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 3cyt
TitleREDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT (HEME PROTEIN)
Function / homology
Function and homology information


mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesThunnus alalunga (albacore)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsTakano, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Redox conformation changes in refined tuna cytochrome c.
Authors: Takano, T. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Conformation Change of Cytochrome C. I. Ferrocytochrome C Structure Refined at 1.5 Angstroms Resolution
Authors: Takano, T. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Conformation Change of Cytochrome C. II. Ferricytochrome C Refinement at 1.8 Angstroms and Comparison with the Ferrocytochrome Structure
Authors: Takano, T. / Dickerson, R.E.
#3: Journal: Sci.Am. / Year: 1980
Title: Cytochrome C and the Evolution of Energy Metabolism
Authors: Dickerson, R.E.
#4: Journal: Nature / Year: 1980
Title: Internal Mobility of Ferrocytochrome C
Authors: Northrup, S.H. / Pear, M.R. / Mccammon, J.A. / Karplus, M. / Takano, T.
#5: Journal: J.Biol.Chem. / Year: 1977
Title: Tuna Cytochrome C at 2.0 Angstroms Resolution. II. Ferrocytochrome Structure Analysis
Authors: Takano, T. / Trus, B.L. / Mandel, N. / Mandel, G. / Kallai, O.B. / Swanson, R. / Dickerson, R.E.
#6: Journal: J.Biol.Chem. / Year: 1977
Title: Tuna Cytochrome C at 2.0 Angstroms Resolution. I. Ferricytochrome Structure Analysis
Authors: Swanson, R. / Trus, B.L. / Mandel, N. / Mandel, G. / Kallai, O.B. / Dickerson, R.E.
#7: Journal: J.Biol.Chem. / Year: 1973
Title: The Structure of Ferrocytochrome C at 2.45 Angstroms Resolution
Authors: Takano, T. / Kallai, O.B. / Swanson, R. / Dickerson, R.E.
#8: Journal: Sci.Am. / Year: 1972
Title: The Structure and History of an Ancient Protein
Authors: Dickerson, R.E.
#9: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionJul 1, 1980Processing site: BNL
SupersessionSep 16, 1980ID: 1CYT
Revision 1.0Sep 16, 1980Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: CYTOCHROME C
I: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0694
Polymers22,8322
Non-polymers1,2372
Water91951
1
O: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0352
Polymers11,4161
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0352
Polymers11,4161
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.420, 74.420, 36.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3944, -0.9189, -0.0029), (-0.9188, 0.3944, -0.0164), (0.0162, -0.0038, -0.9999)
Vector: 37.0557, 37.5607, 17.8347)
DetailsTHE TRANSFORMATION WHICH WILL PLACE THE COORDINATES OF THE OXIDIZED OUTER MOLECULE INTO BEST ALIGNMENT WITH THOSE OF THE OXIDIZED INNER MOLECULE IS GIVEN IN THE MTRIX RECORDS BELOW. THE TRANSFORMATION WHICH WILL PLACE THE COORDINATES OF THE REDUCED MOLECULE (4CYT) INTO BEST ALIGNMENT WITH THOSE OF THE OXIDIZED INNER MOLECULE IN THE SPACE OF THE LATTER IS GIVEN BELOW .2868 .8127 -.5072 47.2662 .5553 -.5724 -.6033 17.5577 -.7806 -.1086 -.6155 16.3160

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Components

#1: Protein CYTOCHROME C


Mass: 11416.114 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thunnus alalunga (albacore) / References: UniProt: P81459
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal grow
*PLUS
Method: other
Details: Takano, T., (1973) J. Biol. Chem., 248, 5234., Swanson, R., (1977) J. Biol. Chem., 252, 759.

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 16831

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Processing

RefinementHighest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 86 51 1743
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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