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- PDB-2lir: NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in... -

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Basic information

Entry
Database: PDB / ID: 2lir
TitleNMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in oxidized states
ComponentsCytochrome c iso-1
KeywordsMETAL TRANSPORT / cytochrome c / P71H / oxidized
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
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 isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLan, W. / Wang, Z. / Yang, Z. / Zhu, J. / Ying, T. / Jiang, X. / Zhang, X. / Wu, H. / Liu, M. / Tan, X. ...Lan, W. / Wang, Z. / Yang, Z. / Zhu, J. / Ying, T. / Jiang, X. / Zhang, X. / Wu, H. / Liu, M. / Tan, X. / Cao, C. / Huang, Z.X.
CitationJournal: Plos One / Year: 2011
Title: Conformational toggling of yeast iso-1-cytochrome C in the oxidized and reduced States.
Authors: Lan, W. / Wang, Z. / Yang, Z. / Zhu, J. / Ying, T. / Jiang, X. / Zhang, X. / Wu, H. / Liu, M. / Tan, X. / Cao, C. / Huang, Z.X.
History
DepositionAug 31, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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 iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6732
Polymers12,0551
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c iso-1


Mass: 12054.726 Da / Num. of mol.: 1 / Mutation: P71H, K72A, C102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#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
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1422D DQF-COSY
1522D 1H-1H NOESY
1622D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM entity_1-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM entity_1-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMentity_1-11
1 mMentity_1-22
Sample conditionsIonic strength: 50mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1747 / NOE intraresidue total count: 667 / NOE long range total count: 462 / NOE medium range total count: 298 / NOE sequential total count: 320
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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