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- PDB-2kxt: NMR structure and calcium-binding properties of the tellurite res... -

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Basic information

Entry
Database: PDB / ID: 2kxt
TitleNMR structure and calcium-binding properties of the tellurite resistance protein TerD from Klebsiella pneumoniae
ComponentsTellurite resistance protein
KeywordsUNKNOWN FUNCTION / KP-TerD / tellurite resistance / Ca2+ binding protein / calcium signaling
Function / homologysav2460 like domains / Lipoxygenase-1 / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPan, Y.R. / Lou, Y.C. / Rizo, J. / Chen, C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: NMR Structure and Calcium-Binding Properties of the Tellurite Resistance Protein TerD from Klebsiella pneumoniae
Authors: Pan, Y.R. / Lou, Y.C. / Seven, A.B. / Rizo, J. / Chen, C.
History
DepositionMay 12, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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: Tellurite resistance protein


Theoretical massNumber of molelcules
Total (without water)21,5861
Polymers21,5861
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tellurite resistance protein


Mass: 21585.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: NTUH-K2044 / Gene: terD / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 DE3 / References: UniProt: C4XDJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The N-terminal 18 residues of KP-TerD are not included in the structural calculation, since they lack of long-range NOEs and have chemical shifts that are similar to those of random coils. ...Details: The N-terminal 18 residues of KP-TerD are not included in the structural calculation, since they lack of long-range NOEs and have chemical shifts that are similar to those of random coils. Please notice that the structure deposit here is from 19 to 192 amino acids of KP-TerD.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CO)CA
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
11113D HBHA(CO)NH
11213D HNHA
11312D 1H-1H NOESY

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Sample preparation

DetailsContents: 20mM potassium phosphate-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 20 mM / Component: potassium phosphate-1
Sample conditionsIonic strength: 0.02 / pH: 7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIA3.1.6Linge, O'Donoghue and Nilgesdata analysis
XwinNMR3.5Bruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
VNMR5Johnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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