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- PDB-1yx0: Solution Structure of Bacillus subtilis Protein ysnE: The Northea... -

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Basic information

Entry
Database: PDB / ID: 1yx0
TitleSolution Structure of Bacillus subtilis Protein ysnE: The Northeast Structural Genomics Consortium Target SR220
Componentshypothetical protein ysnEHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / GFT NMR / Structral Genomics / SR220 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / 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
: / Uncharacterized N-acetyltransferase YsnE
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodSOLUTION NMR / distance geometry simulated annealing torsion angle dynamics
AuthorsLiu, G. / Ma, L. / Shen, Y. / Xiao, R. / Acton, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of Bacillus subtilis Protein ysnE
Authors: Liu, G. / Ma, L. / Shen, Y. / Xiao, R. / Acton, T. / Montelione, G.T. / Szyperski, T.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein ysnE


Theoretical massNumber of molelcules
Total (without water)18,1491
Polymers18,1491
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 #1fewest violations

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Components

#1: Protein hypothetical protein ysnE / Hypothesis


Mass: 18148.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Species: Bacillus subtilis / Strain: subsp. subtilis str. 168 / Gene: ysnE / Production host: Escherichia coli (E. coli) / References: GenBank: 16079885, UniProt: P94562*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (4,3)D HABCAB(CO)NHN
141GFT (4,3) (H)CCH
151Simultaneous Heteronuclear Resolved [1H,1H]-NOESY
NMR detailsText: This structure was determined using GFT NMR techniques.

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Sample preparation

DetailsContents: NMR Buffer 6.5 -- 5% D2O, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P.structure solution
NMRPipe2.3Delaglio, F.processing
XEASY1.3.1.3Bartels, Cdata analysis
DYANA1.5Guentertrefinement
RefinementMethod: distance geometry simulated annealing torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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