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- PDB-2kln: Solution Structure of STAS domain of RV1739c from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2kln
TitleSolution Structure of STAS domain of RV1739c from M. tuberculosis
ComponentsPROBABLE SULPHATE-TRANSPORT TRANSMEMBRANE PROTEIN, COG0659
KeywordsTRANSPORT PROTEIN / SLC26 / Sulfate / SulP / AntiSigma Factor Antagonist / ensemble of 25 structures / Membrane / Transmembrane
Function / homologySTAS domain / Transcription Regulator spoIIAA / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesMycobacterium bovis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
AuthorsSharma, A.K. / Ye, L. / Zolotarev, A.S. / Alper, S.L. / Rigby, A.C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution Structure of the Guanine Nucleotide-binding STAS Domain of SLC26-related SulP Protein Rv1739c from Mycobacterium tuberculosis.
Authors: Sharma, A.K. / Ye, L. / Baer, C.E. / Shanmugasundaram, K. / Alber, T. / Alper, S.L. / Rigby, A.C.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 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_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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PROBABLE SULPHATE-TRANSPORT TRANSMEMBRANE PROTEIN, COG0659


Theoretical massNumber of molelcules
Total (without water)15,0931
Polymers15,0931
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)25 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PROBABLE SULPHATE-TRANSPORT TRANSMEMBRANE PROTEIN, COG0659


Mass: 15093.152 Da / Num. of mol.: 1 / Fragment: residues 437-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Gene: Mb1768c, Rv1739c / Plasmid: pETBlue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3pLacI / References: UniProt: Q7TZN7

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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
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D HNCA
1613D HN(CO)CA
1713D HN(CA)CB
1813D HN(COCA)CB
1913D HNCO
11013D HBHA(CO)NH
11113D H(CCO)NH
11213D C(CO)NH
11313D (H)CCH-TOCSY
11423D HNHA
11513D 1H-15N NOESY
11613D 1H-13C NOESY
11722D 1H-15N HSQC
11823D 1H-15N NOESY
11923D HNHA
12032D 1H-1H TOCSY
12132D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 to 0.8 mM [U-100% 13C; U-100% 15N], STAS domain of Rv1739C, 50 mM sodium phosphate, 275 mM sodium chloride, 2 mM [U-2H] DTT-d10, 0.25 mM DSS, 0.05% w/v sodium azide, 92% H2O/8% D2O92% H2O/8% D2O
20.6 to 0.8 mM [U-100% 15N], STAS domain of Rv1739C, 50 mM sodium phosphate, 275 mM sodium chloride, 2 mM [U-2H] DTT-d10, 0.25 mM DSS, 0.05% w/v sodium azide, 92% H2O/8% D2O92% H2O/8% D2O
30.6 to 0.8 mM STAS domain of Rv1739C-13, 50 mM sodium phosphate, 275 mM sodium chloride, 2 mM [U-2H] DTT-d10, 0.25 mM DSS, 0.05% w/v sodium azide, 92% H2O/8% D2O92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMSTAS domain of Rv1739C-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
275 mMsodium chloride-31
2 mMDTT-d10-4[U-2H]1
0.25 mMDSS-51
0.05 w/vsodium azide-61
0.6 mMSTAS domain of Rv1739C-7[U-100% 15N]2
50 mMsodium phosphate-82
275 mMsodium chloride-92
2 mMDTT-d10-10[U-2H]2
0.25 mMDSS-112
0.05 w/vsodium azide-122
0.6 mMSTAS domain of Rv1739C-133
50 mMsodium phosphate-143
275 mMsodium chloride-153
2 mMDTT-d10-16[U-2H]3
0.25 mMDSS-173
0.05 w/vsodium azide-183
Sample conditionsIonic strength: 275 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2007.030.16.06Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipe2007.030.16.06Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2007.030.16.06Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRDraw3.0 Rev 2007.068.09.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDraw3.0 Rev 2007.068.09.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
ANSIG3.3Kraulisdata analysis
ANSIG3.3Kraulischemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 25

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