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- PDB-2jwg: Structure of a Glycosylphosphatidylinositol-anchored Domain from ... -

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Basic information

Entry
Database: PDB / ID: 2jwg
TitleStructure of a Glycosylphosphatidylinositol-anchored Domain from a Trypanosome Variant Surface Glycoprotein
ComponentsVariant surface glycoprotein ILTAT 1.24
KeywordsMembrane Protein / Immune System / VSG type 1 C-terminal domain
Function / homology
Function and homology information


evasion of host immune response / side of membrane / plasma membrane
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 - #30 / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / ligand-binding face of the semaphorins, domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Variant surface glycoprotein ILTAT 1.24
Similarity search - Component
Biological speciesTrypanosoma (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsJones, N.G. / Nietlispach, D. / Sharma, R. / Burke, D.F. / Eyres, I. / Mues, M. / Mott, H.R. / Carrington, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of a Glycosylphosphatidylinositol-anchored Domain from a Trypanosome Variant Surface Glycoprotein
Authors: Jones, N.G. / Nietlispach, D. / Sharma, R. / Burke, D.F. / Eyres, I. / Mues, M. / Mott, H.R. / Carrington, M.
History
DepositionOct 12, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein ILTAT 1.24


Theoretical massNumber of molelcules
Total (without water)5,1401
Polymers5,1401
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)35 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Variant surface glycoprotein ILTAT 1.24 / VSG


Mass: 5139.770 Da / Num. of mol.: 1 / Fragment: residues 405-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 trxB / References: UniProt: P26329

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM ILTat1.24 C1-domain, 50 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMILTat1.24 C1-domain1
50 mMsodium phosphate1
150 mMsodium chloride1
0.05 %sodium azide1
Sample conditionspH: 6.0 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AZARABoucherprocessing
ANSIGKraulisdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: 786 unambiguous and 192 ambiguous distance restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 35

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