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- PDB-8ok7: Variant Surface Glycoprotein VSG558 NTD -

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Basic information

Entry
Database: PDB / ID: 8ok7
TitleVariant Surface Glycoprotein VSG558 NTD
ComponentsVariant surface glycoprotein 558
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation
Function / homologyTrypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / plasma membrane / Variant surface glycoprotein 558
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZeelen, J.P. / Stebbins, C.E. / van Straaten, M. / Zhong, J.
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 6, 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 558
B: Variant surface glycoprotein 558
C: Variant surface glycoprotein 558
D: Variant surface glycoprotein 558
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,11812
Polymers179,6974
Non-polymers8,4228
Water13,709761
1
A: Variant surface glycoprotein 558
D: Variant surface glycoprotein 558
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8166
Polymers89,8482
Non-polymers3,9684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14640 Å2
ΔGint34 kcal/mol
Surface area31460 Å2
2
B: Variant surface glycoprotein 558
C: Variant surface glycoprotein 558
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3026
Polymers89,8482
Non-polymers4,4544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint32 kcal/mol
Surface area30490 Å2
Unit cell
Length a, b, c (Å)103.080, 64.120, 155.040
Angle α, β, γ (deg.)90.000, 109.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Non-polymers , 2 types, 765 molecules ABCD

#1: Protein
Variant surface glycoprotein 558


Mass: 44924.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: M4T0B2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1_e2-f1WURCSPDB2Glycan 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]{[(2+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.: 3
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: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 2
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

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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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Ada/NaOH 20 % (w/v) PEG 1500 200 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→53.55 Å / Num. obs: 196293 / % possible obs: 98.72 % / Redundancy: 6 % / Biso Wilson estimate: 30.85 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.36
Reflection shellResolution: 1.74→1.8 Å / Num. unique obs: 19469 / CC1/2: 0.268

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Processing

Software
NameVersionClassification
xia2data reduction
PHENIX1.19.2_4158refinement
Coot0.9.8.7 ELmodel building
Aimlessdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→53.55 Å / SU ML: 0.3456 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.0682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 9780 5.04 %
Rwork0.2378 184077 -
obs0.239 193857 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.06 Å2
Refinement stepCycle: LAST / Resolution: 1.74→53.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10900 0 565 761 12226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006411754
X-RAY DIFFRACTIONf_angle_d0.920815893
X-RAY DIFFRACTIONf_chiral_restr0.2481912
X-RAY DIFFRACTIONf_plane_restr0.01042057
X-RAY DIFFRACTIONf_dihedral_angle_d17.49474546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.5662590.53855539X-RAY DIFFRACTION89.64
1.76-1.780.55912750.51295883X-RAY DIFFRACTION93.5
1.78-1.80.49042880.47895915X-RAY DIFFRACTION96.65
1.8-1.830.4693410.46555899X-RAY DIFFRACTION95.35
1.83-1.850.44813200.44626030X-RAY DIFFRACTION97.12
1.85-1.870.44933150.41116085X-RAY DIFFRACTION98.6
1.87-1.90.41413260.38746063X-RAY DIFFRACTION98.63
1.9-1.930.37133520.38216130X-RAY DIFFRACTION98.96
1.93-1.960.36923500.37056108X-RAY DIFFRACTION99.2
1.96-1.990.38743400.37016130X-RAY DIFFRACTION99.37
1.99-2.030.3913600.35466129X-RAY DIFFRACTION99.49
2.03-2.060.36942940.30966194X-RAY DIFFRACTION99.56
2.06-2.10.31073480.29036141X-RAY DIFFRACTION99.75
2.1-2.150.30713120.2856185X-RAY DIFFRACTION99.74
2.15-2.190.28473500.2586142X-RAY DIFFRACTION99.65
2.19-2.240.25533410.25216160X-RAY DIFFRACTION99.51
2.24-2.30.26663140.25386202X-RAY DIFFRACTION99.74
2.3-2.360.27873270.24976180X-RAY DIFFRACTION99.68
2.36-2.430.27463160.24296206X-RAY DIFFRACTION99.8
2.43-2.510.28483110.24896201X-RAY DIFFRACTION99.72
2.51-2.60.25383430.25016162X-RAY DIFFRACTION99.71
2.6-2.70.26843180.24316229X-RAY DIFFRACTION99.73
2.7-2.830.27233240.2326221X-RAY DIFFRACTION99.65
2.83-2.980.25532870.22526232X-RAY DIFFRACTION99.83
2.98-3.160.24353670.22856211X-RAY DIFFRACTION99.94
3.16-3.410.24113550.21146223X-RAY DIFFRACTION99.91
3.41-3.750.20673450.19536243X-RAY DIFFRACTION99.89
3.75-4.290.22513240.1766300X-RAY DIFFRACTION99.91
4.29-5.40.1793400.16966292X-RAY DIFFRACTION99.91
5.41-53.550.20883380.19176442X-RAY DIFFRACTION99.43

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