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- PDB-2kkl: Solution NMR structure of FHA domain of Mb1858 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 2kkl
TitleSolution NMR structure of FHA domain of Mb1858 from Mycobacterium bovis. Northeast Structural Genomics Consortium Target MbR243C (24-155).
ComponentsUncharacterized protein Mb1858
KeywordsStructural Genomics / Unknown function / beta / FHA domain / Phosphoprotein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein Mb1858
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Wang, D. / Foote, E.L. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. ...Yang, Y. / Ramelot, T.A. / Wang, D. / Foote, E.L. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of FHA domain of Mb1858 from Mycobacterium bovis. Northeast Structural Genomics Consortium Target MbR243C (24-155).
Authors: Yang, Y. / Ramelot, T.A. / Wang, D. / Foote, E.L. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 25, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Mb1858


Theoretical massNumber of molelcules
Total (without water)15,2631
Polymers15,2631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein Mb1858


Mass: 15262.847 Da / Num. of mol.: 1 / Fragment: residues 24-155 including FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Gene: Mb1858 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: P64898

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Forkhead-associated (FHA) domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HN(CO)CA
11113D HBHA(CO)NH
11213D H(CCO)NH
11313D C(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11633D (H)CCH-TOCSY
11734D CC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] Mb1858, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM Mb1858, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.1 mM [U-100% 13C; U-100% 15N] Mb1858, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMMb1858-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
1.1 mMMb1858-72
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.1 mMMb1858-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 %sodium azide-183
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure solution
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih-2.20 with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20

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