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- PDB-1fi9: SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 1fi9
TitleSOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / cytochrome c / Solution structure
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / lipid binding / heme binding / apoptotic process / identical protein binding / metal ion 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 / IMIDAZOLE / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodSOLUTION NMR / AMBER
AuthorsBanci, L. / Bertini, I. / Liu, G. / Lu, J. / Reddig, T. / Tang, W. / Wu, Y. / Zhu, D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c
Authors: Banci, L. / Bertini, I. / Liu, G. / Lu, J. / Reddig, T. / Tang, W. / Wu, Y. / Zhu, D.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / 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_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 16, 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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4133
Polymers11,7261
Non-polymers6882
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 400target function
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 / Source: (natural) Equus caballus (horse) / Tissue: HEART / References: UniProt: P00004
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
131DQF-COSY
142DQF-COSY
151TOCSY
162TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
16mM cytochrome c, 1.2M imidazoleH2O
26mM cytochrome c, 1.2M imidazoleD2O
Sample conditionspH: 5.7 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA5Wuthrich et alstructure solution
PSEUDODYANA5Banci et alstructure solution
Amber5PEARLMAN, CASE, CALDWELL, ROSS, CHEATHAM, FERGUSON, SEIBEL, SINGH, WEINER, KOLLMANrefinement
PSEUDOREM5BANCI, BERTINI, GORI SAVELLINI, ROMAGNOLI, TURANO, CREMONINI, LUCHINAT,GARYrefinement
RefinementMethod: AMBER / Software ordinal: 1
Details: OTHER REFINEMENT REMARKS: DYNAMICS SIMULATED ANNEALING,RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION AND IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 35

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