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- PDB-1fhb: THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE CYANIDE ADDUCT OF A M... -

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Entry
Database: PDB / ID: 1fhb
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF THE CYANIDE ADDUCT OF A MET80ALA VARIANT OF SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C. IDENTIFICATION OF LIGAND-RESIDUE INTERACTIONS IN THE DISTAL HEME CAVITY
ComponentsFERRICYTOCHROME C
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR
AuthorsBanci, L. / Bertini, I. / Bren, K.L. / Gray, H.B. / Sompornpisut, P. / Turano, P.
Citation
Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Solution Structure of the Cyanide Adduct of a met80Ala Variant of Saccharomyces Cerevisiae Iso-1-Cytochrome C. Identification of Ligand-Residue Interactions in the Distal Heme Cavity
Authors: Banci, L. / Bertini, I. / Bren, K.L. / Gray, H.B. / Sompornpisut, P. / Turano, P.
#1: Journal: To be Published
Title: Paramagnetic 1H NMR Spectroscopy of the Cyanide Derivative of met80Ala-Iso-1-Cytochrome C
Authors: Bren, K.L. / Gray, H.B. / Banci, L. / Bertini, I. / Turano, P.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structurally Engineered Cytochromes with Unusual Ligand-Binding Properties: Expression of Saccharomyces Cerevisiae met80-->Ala Iso-1-Cytochrome C
Authors: Lu, Y. / Casimilo, D.R. / Bren, K.L. / Richards, J.H. / Gray, H.B.
History
DepositionJun 16, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _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: FERRICYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6723
Polymers12,0301
Non-polymers6432
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / -
Representative

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Components

#1: Protein FERRICYTOCHROME C / MET80ALA-ISO-1-FERRICYTOCHROME C (ISOZYME 1)


Mass: 12029.713 Da / Num. of mol.: 1 / Mutation: H39Q, M80A, C102S
Source method: isolated from a genetically manipulated source
Details: CYANIDE ADDUCT OF ALA 80, ISOZYME 1, OXIDIZED FORM
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: GM3C2 / Variant: H39Q, M80A, C102S / Plasmid: YEP213-LEU58HISCYC1 / Gene (production host): YEAST ISO-1-CYTOCHROME C (CYC1) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00044
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameVersionDeveloperClassification
DIANAGUENTERT,BRAUN,WUTHRICHrefinement
Amber4PEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 17

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