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- PDB-8ok6: Variant Surface Glycoprotein VSG11 two monomers -

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Basic information

Entry
Database: PDB / ID: 8ok6
TitleVariant Surface Glycoprotein VSG11 two monomers
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGkeka, A. / Vlachou, E.P. / Zeelen, J.P. / Stebbins, C.E.
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 1.1Oct 23, 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
C: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,32923
Polymers90,3512
Non-polymers3,97721
Water8,035446
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)141,59233
Polymers135,5273
Non-polymers6,06530
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area19400 Å2
ΔGint-242 kcal/mol
Surface area44190 Å2
MethodPISA
2
C: Variant surface glycoprotein
hetero molecules

C: Variant surface glycoprotein
hetero molecules

C: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,39436
Polymers135,5273
Non-polymers5,86733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18070 Å2
ΔGint-297 kcal/mol
Surface area45040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.244, 76.244, 212.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-504-

SO4

21A-504-

SO4

31A-506-

SO4

41C-509-

SO4

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Variant surface glycoprotein


Mass: 45175.691 Da / Num. of mol.: 2
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

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Sugars , 3 types, 4 molecules

#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-Glycam 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
[]{[(4+1)][b-D-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: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / 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

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Non-polymers , 2 types, 463 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 2.0 M AmmoniumSulfate 100 mM Sodium acetate

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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: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.27 Å / Num. obs: 72926 / % possible obs: 99.75 % / Redundancy: 19 % / Biso Wilson estimate: 32.69 Å2 / CC1/2: 1 / Net I/σ(I): 19.09
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 7093 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
PDB_EXTRACT1.19.2_4158data extraction
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→48.27 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 3646 5 %
Rwork0.2006 69253 -
obs0.2023 72899 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.68 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5540 0 240 446 6226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915910
X-RAY DIFFRACTIONf_angle_d1.17638043
X-RAY DIFFRACTIONf_chiral_restr0.0717960
X-RAY DIFFRACTIONf_plane_restr0.01381021
X-RAY DIFFRACTIONf_dihedral_angle_d15.9142212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.37861350.32992534X-RAY DIFFRACTION94.31
1.77-1.80.33971350.31712580X-RAY DIFFRACTION100
1.8-1.820.3351390.30592631X-RAY DIFFRACTION100
1.82-1.850.31221390.29552648X-RAY DIFFRACTION100
1.85-1.880.37421370.28932601X-RAY DIFFRACTION100
1.88-1.910.30621390.28472645X-RAY DIFFRACTION100
1.91-1.940.32081390.26212643X-RAY DIFFRACTION100
1.94-1.980.27461370.24922593X-RAY DIFFRACTION100
1.98-2.020.2871420.24192691X-RAY DIFFRACTION100
2.02-2.060.29321380.24432631X-RAY DIFFRACTION100
2.06-2.10.25951390.23892631X-RAY DIFFRACTION100
2.1-2.150.23971380.22242631X-RAY DIFFRACTION99.96
2.15-2.210.26291400.2192651X-RAY DIFFRACTION100
2.21-2.270.25321390.21382650X-RAY DIFFRACTION100
2.27-2.330.26521390.21052638X-RAY DIFFRACTION99.96
2.33-2.410.27281400.20622662X-RAY DIFFRACTION100
2.41-2.490.25911400.20222669X-RAY DIFFRACTION100
2.49-2.590.22841410.2082666X-RAY DIFFRACTION100
2.59-2.710.24771410.2062678X-RAY DIFFRACTION100
2.71-2.860.26021400.20222663X-RAY DIFFRACTION99.96
2.86-3.030.22031410.20422683X-RAY DIFFRACTION99.96
3.03-3.270.24181420.19472689X-RAY DIFFRACTION100
3.27-3.60.19211430.17642716X-RAY DIFFRACTION100
3.6-4.120.1971430.16332724X-RAY DIFFRACTION100
4.12-5.190.20761460.16772776X-RAY DIFFRACTION100
5.19-48.270.21981540.20272929X-RAY DIFFRACTION99.81

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