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- PDB-2k2p: Solution NMR structure of protein Atu1203 from Agrobacterium tume... -

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Basic information

Entry
Database: PDB / ID: 2k2p
TitleSolution NMR structure of protein Atu1203 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium (NESG) target AtT10, Ontario Center for Structural Proteomics target ATC1183
ComponentsUncharacterized protein Atu1203
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative metal-binding domain Atu1203 / Ontario Centre for Structural Proteomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HMA domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Gutmanas, A. / Yee, A. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of protein Atu1203 from Agrobacterium tumefaciens.
Authors: Lemak, A. / Gutmanas, A. / Yee, A. / Semesi, A. / Arrowsmith, C.H.
History
DepositionApr 8, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Atu1203


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
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 Uncharacterized protein Atu1203


Mass: 8766.727 Da / Num. of mol.: 1 / Fragment: Residues 18-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_C_2220, Atu1203 / Plasmid: P11 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJD6

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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)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C aliph NOESY
1913D 1H-13C arom NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] Atu1203, 10 mM MOPS, 450 mM sodium chloride, 10 mM DTT, 10 mM benzamidine, 0.01 % NaN3, 10 uM ZnSO4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtu1203[U-13C; U-15N]1
10 mMMOPS1
450 mMsodium chloride1
10 mMDTT1
10 mMbenzamidine1
0.01 %NaN31
10 uMZnSO41
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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / 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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