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- PDB-2kcw: Solution structure of Apo-form YjaB from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2kcw
TitleSolution structure of Apo-form YjaB from Escherichia coli
ComponentsUncharacterized acetyltransferase yjaB
KeywordsTRANSFERASE / GNAT fold / Acyltransferase
Function / homology
Function and homology information


internal peptidyl-lysine acetylation / peptide-lysine-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-lysine N-acetyltransferase YjaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average, model 1
AuthorsLu, J. / Wang, X. / Jin, C.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of Apo-YjaB from Escherichia coli
Authors: Lu, J. / Wang, X. / Xia, B. / Jin, C.
History
DepositionDec 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized acetyltransferase yjaB


Theoretical massNumber of molelcules
Total (without water)16,4651
Polymers16,4651
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)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein Uncharacterized acetyltransferase yjaB


Mass: 16464.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yjaB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P09163, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY

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Sample preparation

DetailsContents: 30mM TRIS, 100mM sodium chloride, 10mM DTT, 1 mM [U-13C; U-15N] YjaB protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
30 mMTRIS1
100 mMsodium chloride1
10 mMDTT1
1 mMYjaB protein[U-13C; U-15N]1
Sample conditionsIonic strength: 130 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
XwinNMR3.5Bruker Biospincollection
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21 / Representative conformer: 1

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