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- PDB-2kj6: NMR Solution Structure of a Tubulin folding cofactor B obtained f... -

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Basic information

Entry
Database: PDB / ID: 2kj6
TitleNMR Solution Structure of a Tubulin folding cofactor B obtained from Arabidopsis thaliana: Northeast Structural Genomics Consortium target AR3436A
ComponentsTubulin folding cofactor B
KeywordsCHAPERONE / Methods development / NESG / AR3436A / Arabidopsis thaliana / Tubulin folding cofactor B / PSI-2 / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


phragmoplast / embryo development ending in seed dormancy / cell division / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-like domain / 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 ...Ubiquitin-like domain / 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-folding cofactor B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMani, R. / Swapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y.J. ...Mani, R. / Swapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y.J. / Acton, T. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of Tbulin folding Cofactor B obtained from Arabidopsis thaliana: Northeast
Authors: Mani, R. / Swapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y.J. / Acton, T. / Rost, B. / Montelione, G.T.
History
DepositionMay 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 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: Tubulin folding cofactor B


Theoretical massNumber of molelcules
Total (without water)10,8521
Polymers10,8521
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 / 140structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tubulin folding cofactor B


Mass: 10852.132 Da / Num. of mol.: 1 / Fragment: sequence database residues 10-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g10220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q67Z52

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a methods development target from the Northeast Structural Genomics Consortium. RMSD of the structure was calculated on only the core residues (13-26,29-37,57-63,67-73,77,88-95) as ...Details: This is a methods development target from the Northeast Structural Genomics Consortium. RMSD of the structure was calculated on only the core residues (13-26,29-37,57-63,67-73,77,88-95) as obtained from FindCore software (Ref: Snyder et al., Proteins: Structure, Function and Bioinformatics, Vol 59, 2005, 673-686).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 1H-15N NOESY
1213D 1H-13Caliphatic NOESY
1313D 1H-13C aromatic NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1632D 1H-15N HSQC
1732D 1H-13C HSQC
1833D HBHA(CO)NH
1933D CBCA(CO)NH
1103(4,3)D GFT-HNNCABCA
1113(4,3)D GFT-CABCA(CO)NHN
11233D HNCO
11333D HNCA
11423D HN(CA)CB
11543D HNHA
11633D H(CCO)NH
11733D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.78 mM [U-100% 13C; U-100% 15N] AR3436A, 90% H2O/10% D2O90% H2O/10% D2O
20.95 mM [U-100% 13C; U-100% 15N] AR3436A, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-100% 13C; U-100% 15N] AR3436A, 90% H2O/10% D2O90% H2O/10% D2O
40.56 mM [U-10% 13C; U-100% 15N] AR3436A, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.78 mMAR3436A-1[U-100% 13C; U-100% 15N]1
0.95 mMAR3436A-2[U-100% 13C; U-100% 15N]2
0.4 mMAR3436A-3[U-100% 13C; U-100% 15N]3
0.56 mMAR3436A-4[U-10% 13C; U-100% 15N]4
Sample conditionsIonic strength: 5mM CaCl2, 10mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and ...Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. The assignments were validated using AVS software. Final structure factors determined using PSVS: ordered residues: 29-33, 15-21, 89-94, 57-62, 39-50, 79-82. Ramachandran statistics for ordered residues: Most favored region: 84.4%, additionally favored region: 15.6%, generously aloowed: 0.1%. Procheck scores for ordered residues (RAW/Z): Phi/psi -0.51/-1.69, all -0.33/-1.95, MolProbity clash scores (RAW/Z) - 15.41/-1.12. RPF scores for the goodness fit to NOESY data: Recall-0.993, Precision-0.878, F-measure-0.932, final dp score-0.756.
NMR constraintsNOE constraints total: 584 / NOE intraresidue total count: 116 / NOE long range total count: 149 / NOE medium range total count: 93 / NOE sequential total count: 226 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 140 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum upper distance constraint violation: 0.2 Å

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