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- PDB-8b3e: Variant Surface Glycoprotein VSG397 -

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Basic information

Entry
Database: PDB / ID: 8b3e
TitleVariant Surface Glycoprotein VSG397
ComponentsVariant surface glycoprotein 397
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein / Trypanosomiasis / Metacyclic / Glycosylation
Function / homologyTrypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / plasma membrane / Variant surface glycoprotein 397
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsZeelen, J.P. / Stebbins, C.E. / Dakovic, S. / Foti, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Negl Trop Dis / Year: 2023
Title: Structural similarities between the metacyclic and bloodstream form variant surface glycoproteins of the African trypanosome.
Authors: Chandra, M. / Dakovic, S. / Foti, K. / Zeelen, J.P. / van Straaten, M. / Aresta-Branco, F. / Tihon, E. / Lubbehusen, N. / Ruppert, T. / Glover, L. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variant surface glycoprotein 397
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8802
Polymers45,4561
Non-polymers4241
Water8,215456
1
A: Variant surface glycoprotein 397
hetero molecules

A: Variant surface glycoprotein 397
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7614
Polymers90,9122
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11000 Å2
ΔGint-22 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.557, 218.484, 66.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

21A-804-

HOH

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Components

#1: Protein Variant surface glycoprotein 397


Mass: 45456.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Trypanosoma brucei (eukaryote) / References: UniProt: M4SY06
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 100 mM SPG Buffer, 21 % (WV) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→66.76 Å / Num. obs: 96793 / % possible obs: 96.37 % / Redundancy: 5.5 % / Biso Wilson estimate: 15.19 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.56
Reflection shellResolution: 1.26→1.305 Å / Num. unique obs: 8421 / CC1/2: 0.219

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
BUCCANEER1.19.2_4158model building
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.26→56.76 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 4807 5.01 %
Rwork0.1828 91190 -
obs0.1845 95997 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.48 Å2 / Biso mean: 27.8077 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.26→56.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 53 456 3346
Biso mean--71.67 33.92 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.270.42851150.38912255237072
1.27-1.290.39341320.38282475260780
1.29-1.310.41781570.36822749290688
1.31-1.320.33741460.34172813295991
1.32-1.340.32491600.3312924308494
1.34-1.360.37111700.30832938310894
1.36-1.380.34481630.29282965312896
1.38-1.40.28031520.27513008316096
1.4-1.420.30591360.26693049318596
1.42-1.440.30381670.25573062322997
1.44-1.470.25741540.22953017317198
1.47-1.490.24181730.21113089326298
1.49-1.520.26021520.20363080323299
1.52-1.550.28391570.206531423299100
1.55-1.590.2651560.189831283284100
1.59-1.620.22731530.182331473300100
1.62-1.670.2341810.174531083289100
1.67-1.710.22511700.174831283298100
1.71-1.760.21951520.17063133328599
1.76-1.820.24631790.1733120329999
1.82-1.880.24921730.179831243297100
1.88-1.960.25281570.17473152330999
1.96-2.050.20351530.17213124327799
2.05-2.150.20211570.1713149330699
2.15-2.290.20432040.170931563360100
2.29-2.470.23171660.17563133329999
2.47-2.710.20151720.163731823354100
2.71-3.110.21231810.16813187336899
3.11-3.910.17671590.153332533412100
3.91-56.760.14891600.16134003560100

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