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- PDB-1xpn: NMR structure of P. aeruginosa protein PA1324: Northeast Structur... -

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Basic information

Entry
Database: PDB / ID: 1xpn
TitleNMR structure of P. aeruginosa protein PA1324: Northeast Structural Genomics Consortium target PaP1
Componentshypothetical protein PA1324Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / b-barrel / Northeast Structural Genomics Consortium / NESG / Protein Structure Initiative / PSI
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Carboxypeptidase regulatory-like domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / Molecular Dynamics, Simulated Annealing
AuthorsCort, J.R. / Ni, S. / Lockert, E.E. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2009
Title: Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170).
Authors: Mercier, K.A. / Cort, J.R. / Kennedy, M.A. / Lockert, E.E. / Ni, S. / Shortridge, M.D. / Powers, R.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: hypothetical protein PA1324


Theoretical massNumber of molelcules
Total (without water)18,4031
Polymers18,4031
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 / 20structures with the lowest energy,structures with the fewest restraint violations
RepresentativeModel #1lowest energy, fewest violations, closest to the average

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Components

#1: Protein hypothetical protein PA1324 / Hypothesis


Mass: 18403.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1324 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I420

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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
1324D-13C,13C-HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-13C,15N PA1324, 20 mM BisTrisPropane, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM U-13C,15N PA1324, 20 mM BisTrisPropane, 100% D2O100% D2O
Sample conditionsIonic strength: 300 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NIH-Xplor2.0.4Brunger, Clore, Kuszewski, Schwieters, Tjandrarefinement
CNS1.1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
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. Final refinement ...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. Final refinement was conducted in explicit solvent with Leonard-Jones and electrostatic potentials. Residues 1-26 are unrestrained and constitute a flexible, n-terminal tail. The structure of residues 27-170 is restrained by 1861 noe distance restraints (541 intraresidue, 513 sequential, 190 medium range, and 617 long range (n>4)), 132 dihedral restraints (65 phi, 67 psi), and 70 h-bond restraints (for 35 h-bonds). Dihedral restraints were derived from Talos and HNHA. H-bond restraints were derived from analysis of amides that exchange slowly with D2O solvent together with initial structures derived from Noesy data.
NMR representativeSelection criteria: lowest energy, fewest violations, closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy,structures with the fewest restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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