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- PDB-8ok4: Variant Surface Glycoprotein VSG11wt-Oil -

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Basic information

Entry
Database: PDB / ID: 8ok4
TitleVariant Surface Glycoprotein VSG11wt-Oil
ComponentsVariant surface glycoprotein
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation
Function / homologyTrypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / side of membrane / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsZeelen, J.P. / Stebbins, C.E. / Aresta-Branco, F. / Foti, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Negl Trop Dis / Year: 2023
Title: A structural classification of the variant surface glycoproteins of the African trypanosomey.
Authors: Dakovic, S. / Zeelen, J.P. / Gkeka, A. / Chandra, M. / van Straaten, M. / Foti, K. / Zhong, J. / Vlachou, E.P. / Aresta-Branco, F. / Verdi, J.P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionMar 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4293
Polymers45,1761
Non-polymers1,2532
Water7,422412
1
A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,2869
Polymers135,5273
Non-polymers3,7596
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area15120 Å2
ΔGint49 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.862, 74.862, 105.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

21A-872-

HOH

31A-977-

HOH

41A-990-

HOH

51A-999-

HOH

61A-1000-

HOH

71A-1011-

HOH

81A-1012-

HOH

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Components

#1: Protein Variant surface glycoprotein


Mass: 45175.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES126.15 / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: B3GVS7
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 1.89 Å3/Da / Density % sol: 34.96 % / Description: hexagonal
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.7 M NaKTartrate, 100 mM Tris/HCl

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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: Sep 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→40.94 Å / Num. obs: 99764 / % possible obs: 99.91 % / Redundancy: 9.4 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.79
Reflection shellResolution: 1.23→1.274 Å / Rmerge(I) obs: 1.777 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 9827 / CC1/2: 0.748

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Coot0.9.8.7 ELmodel building
xia2data reduction
Aimlessdata scaling
SHELXphasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: SAD / Resolution: 1.23→40.94 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 4984 5 %
Rwork0.1618 94780 -
obs0.1631 99764 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.36 Å2 / Biso mean: 22.2497 Å2 / Biso min: 8.93 Å2
Refinement stepCycle: final / Resolution: 1.23→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 154 412 3309
Biso mean--27.28 30.44 -
Num. residues----365
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 (%)
1.23-1.240.33581610.27783088324999
1.24-1.260.29091640.280331203284100
1.26-1.270.31521630.262631163279100
1.27-1.290.23841630.248231113274100
1.29-1.310.29251660.240631523318100
1.31-1.320.29061630.24530943257100
1.32-1.340.3651640.249631233287100
1.34-1.360.28981650.243731403305100
1.36-1.380.27341650.216531513316100
1.38-1.410.22191650.202531383303100
1.41-1.430.25461620.18930813243100
1.43-1.460.2161680.180531763344100
1.46-1.490.22151650.161631303295100
1.49-1.520.21951630.162231313294100
1.52-1.550.1971660.159631533319100
1.55-1.590.19881640.156831153279100
1.59-1.620.18941690.154232033372100
1.62-1.670.16931630.151531023265100
1.67-1.720.20121660.148931453311100
1.72-1.770.19191670.144331703337100
1.77-1.840.17641660.137231623328100
1.84-1.910.16941670.135331683335100
1.91-20.17171670.138631773344100
2-2.10.15351670.139531723339100
2.1-2.230.14671670.130131823349100
2.23-2.410.15471690.138831943363100
2.41-2.650.15691680.148732013369100
2.65-3.030.19731700.158932353405100
3.03-3.820.17221720.147732553427100
3.82-40.940.18391790.177533953574100

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