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- PDB-5cyt: REFINEMENT OF MYOGLOBIN AND CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 5cyt
TitleREFINEMENT OF MYOGLOBIN AND 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: 1.5 Å
AuthorsTakano, T.
Citation
Journal: Methods and Applications in Crystallographic Computing
Year: 1984
Title: Refinement of Myoglobin and Cytochrome C
Authors: Takano, T.
#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: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Redox Conformation Changes in Refined Tuna Cytochrome C
Authors: Takano, T. / Dickerson, R.E.
#4: Journal: Sci.Am. / Year: 1980
Title: Cytochrome C and the Evolution of Energy Metabolism
Authors: Dickerson, R.E.
#5: Journal: Nature / Year: 1980
Title: Internal Mobility of Ferrocytochrome C
Authors: Northrup, S.H. / Pear, M.R. / Mccammon, J.A. / Karplus, M. / Takano, T.
#6: 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.
#7: 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.
#8: 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.
#9: Journal: Sci.Am. / Year: 1972
Title: The Structure and History of an Ancient Protein
Authors: Dickerson, R.E.
#10: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionJan 14, 1988Processing site: BNL
SupersessionJul 12, 1989ID: 4CYT
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 / entity / pdbx_distant_solvent_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 9, 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
R: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0352
Polymers11,4161
Non-polymers6191
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.330, 87.100, 34.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CYTOCHROME C


Mass: 11416.114 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.45 Å3/Da / Density % sol: 49.83 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.159 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 43 91 937

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