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- PDB-1ywu: Solution NMR structure of Pseudomonas Aeruginosa protein PA4608. ... -

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Basic information

Entry
Database: PDB / ID: 1ywu
TitleSolution NMR structure of Pseudomonas Aeruginosa protein PA4608. Northeast Structural Genomics target PaT7
Componentshypothetical protein PA4608Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PA4608 / PaT7 / beta barrel / PilZ domain / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / cyclic-di-GMP binding
Similarity search - Function
Cyclic di-GMP binding protein, PA4608 type / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclic diguanosine monophosphate-binding protein PA4608
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / AutoStructure, simulated annealing, water refinement
AuthorsRamelot, T.A. / Yee, A.A. / Cort, J.R. / Semesi, A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2007
Title: NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein.
Authors: Ramelot, T.A. / Yee, A. / Cort, J.R. / Semesi, A. / Arrowsmith, C.H. / 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: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA4608


Theoretical massNumber of molelcules
Total (without water)17,3071
Polymers17,3071
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein hypothetical protein PA4608 / Hypothesis


Mass: 17307.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4608 / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lamda DE3) / References: UniProt: Q9HVI1

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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-separated NOESY
14313C HSQC
153HNHA
162H/D exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein, U-15N, 13C; 10 mM Tris, 250 mM NaCl, 10 mM DTT, 1 mM benzamidine, 0.01% NaN395% H2O/5% D2O
21 mM protein, U-15N, 13C; 10 mM Tris, 250 mM NaCl, 10 mM DTT, 1 mM benzamidine, 0.01%100% D2O
31 mM protein, U-15N, 10%-13C; 10 mM Tris, 250 mM NaCl, 10 mM DTT, 1 mM benzamidine, 0.01% NaN395% H2O/5% D2O
Sample conditionsIonic strength: 250 mM NaCl / pH: 7.1 / Pressure: ambient / Temperature: 293 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian UNITYVarianUNITY6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipenmrpipe.linuxF. Delaglioprocessing
AutoStructure2.1.0Y.J. Huang, G.T. Montelionedata analysis
X-PLORxplor-nih-2.9.9C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M Clorestructure solution
CNS1.1A. Brungerrefinement
Sparky3.1T. goddard, UCSFdata analysis
RefinementMethod: AutoStructure, simulated annealing, water refinement
Software ordinal: 1
Details: The 22 N-terminal residues (MGSSHHHHHHSSGRENLYFQGH) and 2 C-terminal residues (GS) were not included in the structure calculation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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