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- PDB-1yww: NMR structure of P. aeruginosa protein PA4738: Northeast Structur... -

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Basic information

Entry
Database: PDB / ID: 1yww
TitleNMR structure of P. aeruginosa protein PA4738: Northeast Structural Genomics Consortium target PaP2
ComponentsHypothetical protein PA4738Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YjbJ / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYjbJ / CsbD-like domain / Stress response protein YjbJ / YjbJ superfamily / CsbD-like / Protein Yjbj; Chain: A; / Orthogonal Bundle / Mainly Alpha / UPF0337 protein PA4738
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / Molecular Dynamics, Simulated Annealing
AuthorsCort, J.R. / Ni, S. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of Pseudomonas aeruginosa protein PA4738
Authors: Cort, J.R. / Ni, S. / Montelione, G.T. / Kennedy, M.A.
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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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 PA4738


Theoretical massNumber of molelcules
Total (without water)9,7961
Polymers9,7961
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 / 23low energy structures with fewest restraint violations
RepresentativeModel #1low energy, few violations, close to average

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Components

#1: Protein Hypothetical protein PA4738 / Hypothesis


Mass: 9795.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4738 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HV61

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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
1324D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-13C, 15N PA4738, 1.0 M NaCl, 20 mM Tris, pH 7.890% H2O/10% D2O
21 mM U-13C, 15N PA4738, 1.0 M NaCl, 20 mM Tris, pH 7.8100% D2O
Sample conditionsIonic strength: 1 Molar NaCl / pH: 7.8 / 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 INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-XplorBrunger,Clore,Kuszewski,Schwieters, Tjandrarefinement
Sparky3.106T.D. Goddard, D.G. Knellerdata analysis
AutoStructure2.1.0G.T. Montelione, J.Y. Huangstructure solution
TALOS2003G. Cornilescu, F. Delaglio, A. Baxdata analysis
RefinementMethod: Molecular Dynamics, Simulated Annealing / Software ordinal: 1
Details: NOE distance restraints were determined automatically using AutoStructure (G.T. Montelione & Y.J. Huang) starting from peak-picked NOESY data and chemical shift assignments.
NMR representativeSelection criteria: low energy, few violations, close to average
NMR ensembleConformer selection criteria: low energy structures with fewest restraint violations
Conformers calculated total number: 23 / Conformers submitted total number: 20

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