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- PDB-1cyc: THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3... -

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Entry
Database: PDB / ID: 1cyc
TitleTHE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION
ComponentsFERROCYTOCHROME C
KeywordsELECTRON TRANSPORT
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 speciesKatsuwonus pelamis (skipjack tuna)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTanaka, N. / Yamane, T. / Tsukihara, T. / Ashida, T. / Kakudo, M.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1975
Title: The crystal structure of bonito (katsuo) ferrocytochrome c at 2.3 A resolution. II. Structure and function.
Authors: Tanaka, N. / Yamane, T. / Tsukihara, T. / Ashida, T. / Kakudo, M.
#1: Journal: J.Biochem.(Tokyo) / Year: 1973
Title: Oxidation of a Ferrocytochrome C in the Crystalline State-Structural Change and Anion Binding
Authors: Tsukihara, T. / Yamane, T. / Tanaka, N. / Ashida, T. / Kakudo, M.
#2: Journal: J.Biochem.(Tokyo) / Year: 1973
Title: The Crystal Structure of Bonito (Katsuo) Ferrocytochrome C at 2.3 Angstroms Resolution
Authors: Ashida, T. / Tanaka, N. / Yamane, T. / Tsukihara, T. / Kakudo, M.
#3: Journal: J.Biochem.(Tokyo) / Year: 1971
Title: The Crystal Structure of Bonito (Katsuo) Ferrocytochrome C at 4 Angstroms Resolution
Authors: Ashida, T. / Ueki, T. / Tsukihara, T. / Sugihara, A. / Takano, T. / Kakudo, M.
#4: Journal: J.Biochem.(Tokyo) / Year: 1971
Title: The Amino Acid Sequence of Cytochrome C from Bonito (Katsuwonus Pelamis, Linnaeus)
Authors: Nakayama, T. / Titani, K. / Narita, K.
#5: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#6: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionAug 1, 1976Processing site: BNL
Revision 1.0Oct 6, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / 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_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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
A: FERROCYTOCHROME C
B: FERROCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0454
Polymers22,8082
Non-polymers1,2372
Water181
1
A: FERROCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0232
Polymers11,4041
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERROCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0232
Polymers11,4041
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.680, 84.580, 37.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1) / Vector: 28.84)

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Components

#1: Protein FERROCYTOCHROME C


Mass: 11404.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Katsuwonus pelamis (skipjack tuna) / References: UniProt: P00025
#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.: 1 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal grow
*PLUS
Method: other / Details: Ashida, T., (1971) J. Biochem., 70, 913.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 86 1 1677

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