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- PDB-2k4v: Solution structure of uncharacterized protein PA1076 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2k4v
TitleSolution structure of uncharacterized protein PA1076 from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium (NESG) target PaT3, Ontario Center for Structural Proteomics target PA1076 .
Componentsuncharacterized protein PA1076
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyDomain of unknown function DUF5064 / Protein of unknown function DUF5064 / Domain of unknown function (DUF5064) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGutmanas, A. / Lemak, A. / Fares, C. / Yee, A. / Semesi, A. / Arrowsmith, C.H. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of uncharacterized protein PA1076 from Pseudomonas aeruginosa.
Authors: Gutmanas, A. / Lemak, A. / Fares, C. / Yee, A. / Semesi, A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJun 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein PA1076


Theoretical massNumber of molelcules
Total (without water)14,2341
Polymers14,2341
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein uncharacterized protein PA1076


Mass: 14233.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species: aeruginosa / Gene: PA1076 / Plasmid: p11 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / Variant (production host): star magic / References: UniProt: Q9I4Q3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D HNCO
1613D HNCA
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-13C aromatic NOESY
11413D H(C)CH-TOCSY aromatic
11513D (H)CCH-TOCSY aromatic
1161T1rho array
11713D IPAP E-COSY HNCO
11813D IPAP E-COSY HNCO
NMR detailsText: 5 mm Shigemi tube Most 3D spectra collected using non-uniform sampling and processed with MDDNMR

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Sample preparation

DetailsContents: 0.7-1 mM [U-100% 13C; U-100% 15N] PA1076, 1x inhibitor cocktail (purchased from Roche), 10 mM [U-2H] TRIS, 300 mM sodium chloride, 0.01 % sodium azide, 1 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMPA1076[U-100% 13C; U-100% 15N]1
10 mMTRIS[U-2H]1
300 mMsodium chloride1
0.01 %sodium azide1
1 mMbenzamidine1
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis1.4CCPNpeak picking
CcpNmr Analysis1.4CCPNchemical shift assignment
MddNMR1.2cV. Orekhov, I. Ibraghimovprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
ABACUSA. Lemakchemical shift assignment
ABACUSA. Lemaknoe assignment
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement with RDC constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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