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- PDB-2duw: Solution structure of putative CoA-binding protein of Klebsiella ... -

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Basic information

Entry
Database: PDB / ID: 2duw
TitleSolution structure of putative CoA-binding protein of Klebsiella pneumoniae
Componentsputative CoA-binding protein
KeywordsLIGAND BINDING PROTEIN / Klebsiella pneumoniae / putative CoA-binding protein
Function / homologyCoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CoA_binding domain-containing protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsHung, K.W. / Lin, Y.C. / Cheng, C.C. / Chang, C.F. / Tsai, S.F. / Huang, T.H.
CitationJournal: To be Published
Title: Solution structure of putative CoA-binding protein of Klebsiella pneumoniae
Authors: Hung, K.W. / Lin, Y.C. / Cheng, C.C. / Fang, P.J. / Chang, C.F. / Tsai, S.F. / Huang, T.H.
History
DepositionJul 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE A sequence database reference for this protein does not currently exist. 8 residues in the ...SEQUENCE A sequence database reference for this protein does not currently exist. 8 residues in the C terminus were cloning artifacts.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein putative CoA-binding protein


Mass: 15803.228 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A6T758

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM putative CoA binding protein, U-15N, 13C; 20mM Tris-HCl Buffer Containing 50mM NaCl, 50mM Glu and 50mM Arg, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM Tris-HCl Buffer Containing 50mM NaCl, 50mM Glu and 50mM Arg
pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
Sparky3.112T.D. Goddard and D.G. Knellerdata analysis
CYANA2.1Peter Guntertstructure solution
CYANA2.1Peter Guntertrefinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on 1912 distance constraints and 150 angle constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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