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- PDB-2giw: SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, 40 S... -

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Basic information

Entry
Database: PDB / ID: 2giw
TitleSOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, 40 STRUCTURES
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / CYTOCHROME C
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / heme binding / lipid binding / metal ion binding ...cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / heme binding / lipid binding / metal ion binding / identical protein binding / cytosol
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 speciesEquus caballus (horse)
MethodSOLUTION NMR / SIMULATED ANNEALING TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
AuthorsBanci, L. / Bertini, I. / Huber, J.G. / Spyroulias, G.A. / Turano, P.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 1999
Title: Solution structure of reduced horse heart cytochrome c.
Authors: Banci, L. / Bertini, I. / Huber, J.G. / Spyroulias, G.A. / Turano, P.
#1: Journal: Biochemistry / Year: 1997
Title: Solution Structure of Oxidized Horse Heart Cytochrome C
Authors: Banci, L. / Bertini, I. / Gray, H.B. / Luchinat, C. / Reddig, T. / Rosato, A. / Turano, P.
#2: Journal: Biochemistry / Year: 1994
Title: Solution Structure of Horse Heart Ferrocytochrome C Determined by High-Resolution NMR and Restrained Simulated Annealing
Authors: Qi, P.X. / Di Stefano, D.L. / Wand, A.J.
History
DepositionJun 25, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / 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_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3442
Polymers11,7261
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein CYTOCHROME C


Mass: 11725.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED / Source: (natural) Equus caballus (horse) / Organ: HEART / References: UniProt: P00004
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NOES OF 1H NMR.

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 100 mM PHOSPHATE / pH: 7 / Pressure: 1013 mbar / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE 800 / Manufacturer: Bruker / Model: AVANCE 800 / Field strength: 800 MHz

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
Amberstructure solution
RefinementMethod: SIMULATED ANNEALING TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 40 / Conformers submitted total number: 40

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