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- PDB-1lc2: Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Ace... -

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Basic information

Entry
Database: PDB / ID: 1lc2
TitleSolution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR 30 Structures
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / CYTOCHROME C / ORGANIC SOLVENT
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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / 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 / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
AuthorsSivakolundu, S.G. / Mabrouk, P.A.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2003
Title: Structure function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution
Authors: Sivakolundu, S.G. / Mabrouk, P.A.
History
DepositionApr 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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

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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)12,3442
Polymers11,7261
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein CYTOCHROME C / / FERROCYTOCHROME C


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


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 5mM FERROCYTOCHROME C 1H; 50mM PHOSPHATE BUFFER; 70% H2O, 30% CD3CN
Solvent system: 70% H2O, 30% CD3CN
Sample conditionsIonic strength: 50mM / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Home-built HOME BUILT / Manufacturer: Home-built / Model: HOME BUILT / Field strength: 591.1 MHz

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Processing

NMR software
NameVersionDeveloperClassification
RNMR1David Rubencollection
Felix2000MSIprocessing
DYANA1.5Guntert, P., Mumenthaler, C. & Wuthrich, K.structure solution
Amber5CASE, PEARLMAN, CALDWELL, CHEATHAM III, ROSS, SIMMERLING, DARDEN, MERZ, STANTON, CHENG, VINCENT, CROWLEY, FERGUSON, RADMER, SEIBEL, SINGH, WEINER, KOLLMANrefinement
Amber5structure solution
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
Software ordinal: 1
Details: The structures are based on a total of 2232 NOE-based distance restraints and 73 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 30

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