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- PDB-1ocd: CYTOCHROME C (OXIDIZED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERA... -

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Basic information

Entry
Database: PDB / ID: 1ocd
TitleCYTOCHROME C (OXIDIZED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT
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 / lipid binding / heme 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 / lipid binding / heme 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 / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsQi, P.X. / Beckman, R.A. / 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 Ferricytochrome C
Authors: Feng, Y. / Roder, H. / Englander, S.W. / Wand, A.J. / Di Stefano, D.L.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jun 16, 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
Revision 1.4Mar 14, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / pdbx_nmr_ensemble ...citation / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly_prop
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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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
Buried area1100 Å2
ΔGint-23 kcal/mol
Surface area6350 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 64structures with the least restraint violations
RepresentativeModel #1fewest violations

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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: OXIDIZED / 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
#3: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
1423D NOESY-TOCSY
151DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1[U-15N] 7-10 mM cytochrome c, 50 mM potassium phosphatesample_190% H2O/10% D2O
solution2[U-13C; U-15N] 15 mM cytochrome c, 50 mM potassium phosphatesample_290% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMcytochrome c[U-15N]7-101
50 mMpotassium phosphatenatural abundance1
15 mMcytochrome c[U-13C; U-15N]2
50 mMpotassium phosphatenatural abundance2
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 AMBrukerAM6001
Bruker AMXBrukerAMX5002
Bruker AMBrukerAM3003

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
DSPACEHare Researchstructure solution
X-PLORBRUNGERstructure solution
FelixBiosym Technologies Inc.data analysis
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 64 / Conformers submitted total number: 1

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