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- PDB-2k54: Solution NMR structure of protein Atu0742 from Agrobacterium Tume... -

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Basic information

Entry
Database: PDB / ID: 2k54
TitleSolution NMR structure of protein Atu0742 from Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium (NESG0) target AtT8. Ontario Center for Structural Proteomics target ATC0727 .
ComponentsProtein Atu0742
Keywordsstructural genomics / unknown function / protein of unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised conserved protein UCP030561 / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLemak, A. / Yee, A. / Gutmanas, A. / Fares, C. / Semesi, A. / Arrowsmith, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution structure of protein ATC0727 from Agrobacterium Tumefaciens.
Authors: Lemak, A. / Yee, A. / Gutmanas, A. / Fares, C. / Semesi, A. / Arrowsmith, C.
#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 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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: Protein Atu0742


Theoretical massNumber of molelcules
Total (without water)14,0761
Polymers14,0761
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 Protein Atu0742


Mass: 14075.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: tumefaciens / Strain: C58 / Gene: AGR_C_1343, Atu0742 / Plasmid: p15Tv lic / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJY7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D 1H-15N NOESY
1613D (H)CCH-TOCSY
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-13C arom NOESY
11012D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] Atu0742, 10 mM mops, 450 mM potassium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtu0742[U-13C; U-15N]1
10 mMmops1
450 mMpotassium chloride1
10 uMZnSO41
10 mMDTT1
0.01 %NaN31
10 mMbenzamidine1
Sample conditionsIonic strength: 450 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Arrowsmith,Llinaschemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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