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- PDB-1r57: NMR Solution Structure of a GCN5-like putative N-acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 1r57
TitleNMR Solution Structure of a GCN5-like putative N-acetyltransferase from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR31
Componentsconserved hypothetical protein
KeywordsTRANSFERASE / GCN5 / N-acetyltransferase / Structural genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Yjdj-type Gcn5-related N-acetyltransferase / GCN5-related N-acetyl-transferase / Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyltransferase domain-containing protein / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / automated generation of initial distance restraint set distance geometry simulated annealing final refinement in explicit solvent
AuthorsCort, J.R. / Acton, T.B. / Ma, L. / Xiao, R.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2008
Title: Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins.
Authors: Cort, J.R. / Ramelot, T.A. / Murray, D. / Acton, T.B. / Ma, L.C. / Xiao, R. / Montelione, G.T. / Kennedy, M.A.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity_poly / pdbx_database_related / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _pdbx_database_related.db_id ..._entity_poly.pdbx_target_identifier / _pdbx_database_related.db_id / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 999sequence The protein that is the subject of this structure determination was cloned from ...sequence The protein that is the subject of this structure determination was cloned from Staphylococcus aureus subsp. Rosenbach. This strain has not been the subject of genome sequencing, however three other strains have been sequenced: MW2, Mu50,and N315. The amino acid residues at three positions in the protein structure described here differ from those at some or all of the same positions in the sequences from the three sequenced strains. These mutations, indicated by the notation XnY where the X is the residue in the sequenced strain, n is the position number, and Y is the residue in the structure described here, are as follows: Strain MW2: V57L and H68N Strains Mu50 and N315: H21N, V57L, and H68N

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)11,6321
Polymers11,6321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with fewest restraint violations and lowest energy
RepresentativeModel #1similarity to average, few violations, and low energy

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Components

#1: Protein conserved hypothetical protein


Mass: 11631.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SA2309 or MW2441 or SAV2521 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99RB4, UniProt: A0A0H3JTC0*PLUS, 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
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
143HNHB
1524D 13C-separated NOESY
NMR detailsText: amide proton exchange was measured by dissolving a lyophilized protonated sample in D2O

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein U-15N,13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
21 mM protein U-15N,13C, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 0.02% NaN3; 100% D2O100% D2O
30.4 mM protein U-15N,5%-13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: .115 / pH: 6.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure1.1Huang, Tejero, Montelionedata analysis
CNS1.1Brunger, Schwieters, Kuszewski, Tjandra, Clorestructure solution
CNS1.1Brungerrefinement
Felix97MSIprocessing
Sparky3Goddard, Knellerdata analysis
TALOSCornilescu, Delaglio, Baxdata analysis
RefinementMethod: automated generation of initial distance restraint set distance geometry simulated annealing final refinement in explicit solvent
Software ordinal: 1
Details: Backbone and sidechain assignments were determined manually from triple-resonance NMR data. NOE distance restraints were derived automatically from peak-picked data with AutoStructure, then ...Details: Backbone and sidechain assignments were determined manually from triple-resonance NMR data. NOE distance restraints were derived automatically from peak-picked data with AutoStructure, then error-checked and corrected manually. The structure is based on 848 restraints: 710 meaningful distance restraints, 58 hydrogen bond restraints, and 80 dihedral angle restraints. There are 9.5 restraints per restrained residue. Phi dihedral restraints were derived from the HNHA experiment and TALOS. Psi dihedral restraints were derived from NOE ratios, secondary structure propensities evident in preliminary structures, alpha carbon chemical shifts, and TALOS. Residues 44-51 comprise a poorly-defined loop in this ensemble of structures. Residues 1-3 and 94-102 are unstructured termini.
NMR representativeSelection criteria: similarity to average, few violations, and low energy
NMR ensembleConformer selection criteria: structures with fewest restraint violations and lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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