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- PDB-1dvv: SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FR... -

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Basic information

Entry
Database: PDB / ID: 1dvv
TitleSOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA
ComponentsCYTOCHROME C551
KeywordsELECTRON TRANSPORT / cytochrome c / stability
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c-551
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHasegawa, J. / Uchiyama, S. / Tanimoto, Y. / Mizutani, M. / Kobayashi, Y. / Sambongi, Y. / Igarashi, Y.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Selected mutations in a mesophilic cytochrome c confer the stability of a thermophilic counterpart.
Authors: Hasegawa, J. / Uchiyama, S. / Tanimoto, Y. / Mizutani, M. / Kobayashi, Y. / Sambongi, Y. / Igarashi, Y.
History
DepositionJan 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C551
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3412
Polymers8,7251
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
Representative

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Components

#1: Protein CYTOCHROME C551


Mass: 8724.947 Da / Num. of mol.: 1 / Mutation: F7A, V13M, F34Y, E43Y, V78I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00099
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122DQF-COSY
1333D 15N-separated NOESY
143HNHA
153HNHB
1643D 13C,15N simultanously separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite90% H2O/10% D2O
21mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite100% D2O
31mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N reduced with dithionite90% H2O/10% D2O
41mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N,13C reduced with dithionite90% H2O/10% D2O
Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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