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- PDB-2kjr: Solution NMR structure of the N-terminal Ubiquitin-like Domain fr... -

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Basic information

Entry
Database: PDB / ID: 2kjr
TitleSolution NMR structure of the N-terminal Ubiquitin-like Domain from Tubulin-binding Cofactor B, CG11242, from Drosophila melanogaster. Northeast Structural Genomics Consortium Target FR629A (residues 8-92)
ComponentsCG11242
KeywordsCHAPERONE / ubl / ubiquitin / ubiquitin-like / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SIGNALING PROTEIN
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / oocyte axis specification / establishment of apical/basal cell polarity / microtubule plus-end / tubulin complex assembly / microtubule plus-end binding / alpha-tubulin binding / cytoplasmic microtubule organization / mitotic spindle / cell cortex ...post-chaperonin tubulin folding pathway / oocyte axis specification / establishment of apical/basal cell polarity / microtubule plus-end / tubulin complex assembly / microtubule plus-end binding / alpha-tubulin binding / cytoplasmic microtubule organization / mitotic spindle / cell cortex / centrosome / nucleus / cytoplasm
Similarity search - Function
Tubulin-folding cofactor B, N-terminal ubiquitin-like domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Tubulin-folding cofactor B, N-terminal ubiquitin-like domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tubulin-binding cofactor B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. ...Ramelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / 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 the N-terminal Ubiquitin-like Domain from Tubulin-binding Cofactor B, CG11242, from Drosophila melanogaster. Northeast Structural Genomics Consortium Target FR629A (residues 8-92)
Authors: Ramelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 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: database_2 / pdbx_database_status ...database_2 / 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: CG11242


Theoretical massNumber of molelcules
Total (without water)10,3611
Polymers10,3611
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 / 125structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CG11242


Mass: 10360.654 Da / Num. of mol.: 1 / Fragment: ubl domain, residues 8-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG11242, Dmel_CG11242 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: A1ZBM2

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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
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D C(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-TOCSY
11322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM MES, 50 mM arginine, 10 mM DTT, 0.02 % sodium azide, 1.1 mM [U-100% 13C; U-100% 15N] protein, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
250 mM MES, 50 mM arginine, 10 mM DTT, 0.02 % sodium azide, 1.0 mM [U-5% 13C; U-100% 15N] protein, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMMES1
50 mMarginine1
10 mMDTT1
0.02 %sodium azide1
1.1 mMprotein[U-100% 13C; U-100% 15N]1
50 uMDSS1
50 mMMES2
50 mMarginine2
10 mMDTT2
0.02 %sodium azide2
1.0 mMprotein[U-5% 13C; U-100% 15N]2
50 uMDSS2
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
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
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PDBStat) R. Tejero, G.T. Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NIH-Xplor-2.20 refinement with hydrogen bond PMF, radius of gyration, rama, IVM module.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 20

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