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- PDB-1fi3: SOLUTION STRUCTURE OF THE M61H MUTANT OF PSEUDOMONAS STUTZERI SUB... -

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Basic information

Entry
Database: PDB / ID: 1fi3
TitleSOLUTION STRUCTURE OF THE M61H MUTANT OF PSEUDOMONAS STUTZERI SUBSTRAIN ZOBELL FERROCYTOCHROME C-551
ComponentsCYTOCHROME C-551
KeywordsELECTRON TRANSPORT / c-551 family
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / 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-551
Similarity search - Component
Biological speciesPseudomonas stutzeri ZoBell (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsMiller, G.T. / Hardman, J.K. / Timkovich, R.
CitationJournal: Biophys.J. / Year: 2001
Title: Solution conformation of the Met 61 to His 61 mutant of Pseudomonas stutzeri ZoBell ferrocytochrome c-551.
Authors: Miller, G.T. / Hardman, J.K. / Timkovich, R.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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_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-551
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1982
Polymers8,5801
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein CYTOCHROME C-551 / C551 / CYTOCHROME C8


Mass: 8579.808 Da / Num. of mol.: 1 / Mutation: M61H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri ZoBell (bacteria) / Species: Pseudomonas stutzeri / Strain: ZOBELL / Plasmid: PCATNIRMM61H / Production host: Escherichia coli (E. coli) / References: UniProt: P00101
#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 experimentType: NOESY, HOHAHA, DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5 mM c-551; 50 mM phosphate buffer, sodium dithionite
Solvent system: D2O or 10%D2O
Sample conditionspH: 9.2 / Temperature: 333 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM / Manufacturer: Bruker / Model: AM / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Hare/Reedprocessing
CNSsolve0.9aBrungerstructure solution
CNSsolve0.9aBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1039 NOE distance constraints 35 H-bond constraints 72 torsion angle main chain constraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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