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- PDB-1m60: Solution Structure of Zinc-substituted cytochrome c -

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Basic information

Entry
Database: PDB / ID: 1m60
TitleSolution Structure of Zinc-substituted cytochrome c
ComponentsZinc-substituted cytochrome c
KeywordsELECTRON TRANSPORT / six-coordinated zinc cyt c
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
ZINC SUBSTITUTED HEME C / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsQian, C. / Yao, Y. / Tong, Y. / Wang, J. / Tang, W.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Structural analysis of zinc-substituted cytochrome c.
Authors: Qian, C. / Yao, Y. / Tong, Y. / Wang, J. / Tang, W.
History
DepositionJul 11, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2002Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Zinc-substituted cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3542
Polymers11,7261
Non-polymers6281
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein Zinc-substituted 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-HES / ZINC SUBSTITUTED HEME C


Mass: 628.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34N4O4Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: 5mM Zn-cytc / Solvent system: 90% H2O, 10% D2O; 90% D2O, 10% D2O
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 293 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: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Guentert / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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