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- PDB-2mek: N-terminal domain of Bilbo1 from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 2mek
TitleN-terminal domain of Bilbo1 from Trypanosoma brucei
ComponentsN-TERMINAL DOMAIN OF BILBO1
KeywordsMETAL BINDING PROTEIN / Bilbo1 / N-terminal domain
Function / homology
Function and homology information


cilium organization / calcium ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #650 / BILBO1, N-terminal domain / BILBO1 N-terminal domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Ubiquitin-like (UB roll) / EF-hand calcium-binding domain profile. / EF-hand domain ...Ubiquitin-like (UB roll) - #650 / BILBO1, N-terminal domain / BILBO1 N-terminal domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Ubiquitin-like (UB roll) / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsVidilaseris, K. / Morriswood, B. / Kontaxis, G. / Dong, G.
CitationJournal: To be Published
Title: Structure and assembly mechanism of TbBILBO1, an essential flagellar pocket collar protein
Authors: Vidilaseris, K. / Morriswood, B. / Kontaxis, G. / Dong, G.
History
DepositionSep 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-TERMINAL DOMAIN OF BILBO1


Theoretical massNumber of molelcules
Total (without water)12,9001
Polymers12,9001
Non-polymers00
Water0
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 N-TERMINAL DOMAIN OF BILBO1


Mass: 12899.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb11.01.3960 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q382W6

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D HCACO
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] BILBO1-NTD, 20 mM sodium phosphate, 100 mM sodium chloride, 10 % [U-2H] D2O, 0.2 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBILBO1-NTD-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
10 %D2O-4[U-2H]1
0.2 %sodium azide-51
Sample conditionspH: 7.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA8001
Varian Direct DriveVarianDirect Drive6002
Varian InovaVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / 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

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