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- PDB-2k7i: Solution NMR structure of protein ATU0232 from AGROBACTERIUM TUME... -

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Basic information

Entry
Database: PDB / ID: 2k7i
TitleSolution NMR structure of protein ATU0232 from AGROBACTERIUM TUMEFACIENS. Northeast Structural Genomics Consortium (NESG) target AtT3. Ontario Center for Structural Proteomics target ATC0223.
ComponentsUPF0339 protein Atu0232
Keywordsstructural genomics / unknown function / protein of unknown function / swapped dimer. PSI2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYegP-like / : / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / UPF0339 protein Atu0232
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Srisailam, S. / Yee, A. / Bansal, S. / Semesi, A. / Prestegard, J. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution structure of protein ATU0232 from Agrobacterium Tumefaciens.
Authors: Lemak, A. / Srisailam, S. / Yee, A. / Bansal, S. / Semesi, A. / Prestegard, J. / 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
DepositionAug 12, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 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 / Other
Category: 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: UPF0339 protein Atu0232
B: UPF0339 protein Atu0232


Theoretical massNumber of molelcules
Total (without water)18,7552
Polymers18,7552
Non-polymers00
Water00
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 UPF0339 protein Atu0232


Mass: 9377.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: tumefaciens / Strain: C58 / Gene: Atu0232, AGR_C_390 / Plasmid: p15Tv lic / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UIR1

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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 (H)C(CO)NH TOCSY
1613D H(CCO)NH TOCSY
1723D (H)CCH-TOCSY
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11123D 1H-13C NOESY
11213D 1H-13C arom NOESY
11312D 1H-15N HSQC(IPAP)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] Atu0232, 10 mM TRIS, 500 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM Benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] Atu0232, 10 mM TRIS, 500 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM Benzamidine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtu0232[U-13C; U-15N]1
10 mMTRIS1
500 mMsodium chloride1
10 uMZnSO41
10 mMDTT1
0.01 %NaN31
10 mMBenzamidine1
0.5 mMAtu0232[U-13C; U-15N]2
10 mMTRIS2
500 mMsodium chloride2
10 uMZnSO42
10 mMDTT2
0.01 %NaN32
10 mMBenzamidine2
Sample conditionsIonic strength: 500 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Llinas, Arrowsmithresonance assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: molecular dynamics in water bath with RDC restraints
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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