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- PDB-2frc: CYTOCHROME C (REDUCED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAG... -

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Basic information

Entry
Database: PDB / ID: 2frc
TitleCYTOCHROME C (REDUCED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT
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 / SIMMULATED ANNEALING
AuthorsQi, P.X. / Di Stefano, D.L. / Wand, A.J.
Citation
Journal: Biochemistry / Year: 1996
Title: Solution structure of horse heart ferricytochrome c and detection of redox-related structural changes by high-resolution 1H NMR.
Authors: Qi, P.X. / Beckman, R.A. / Wand, A.J.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Structural Water in Oxidized and Reduced Horse Heart Cytochrome C
Authors: Qi, P.X. / Urbauer, J.L. / Fuentes, E.J. / Leopold, M.F. / Wand, A.J.
#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.
#3: Journal: Biochemistry / Year: 1989
Title: Proton Resonance Assignments of Horse Ferrocytochrome C
Authors: Wand, A.J. / Di Stefano, D.L. / Feng, Y.Q. / Roder, H. / Englander, S.W.
History
DepositionJul 2, 1996Processing site: BNL
SupersessionJul 29, 1997ID: 1FRC
Revision 1.0Jul 29, 1997Provider: 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 / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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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
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 256LOWEST PENALTY
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 / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121NOESY
131TOCSY
141NOESY

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Sample preparation

Sample conditionspH: 5.7 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMBrukerAM6002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
FELIX/DSPACE/XPLOR/ANCILLstructure solution
RefinementMethod: SIMMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST PENALTY / Conformers calculated total number: 256 / Conformers submitted total number: 1

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