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- PDB-8ok5: Variant Surface Glycoprotein VSG11 monomer with iodine -

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Basic information

Entry
Database: PDB / ID: 8ok5
TitleVariant Surface Glycoprotein VSG11 monomer with iodine
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 / IODIDE ION / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsZeelen, J.P. / Stebbins, C.E. / Aresta-Branco, F.
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 13, 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)48,16024
Polymers44,2421
Non-polymers3,91823
Water8,143452
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)144,48072
Polymers132,7263
Non-polymers11,75469
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23180 Å2
ΔGint27 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.426, 75.426, 106.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Components on special symmetry positions
IDModelComponents
11A-502-

IOD

21A-508-

IOD

31A-518-

IOD

41A-725-

HOH

51A-917-

HOH

61A-988-

HOH

71A-995-

HOH

81A-1007-

HOH

91A-1027-

HOH

101A-1050-

HOH

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Components

#1: Protein Variant surface glycoprotein


Mass: 44241.941 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: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 1.98 Å3/Da / Density % sol: 37.74 % / 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: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→41.26 Å / Num. obs: 93126 / % possible obs: 99.96 % / Redundancy: 9.7 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.999 / Net I/av σ(I): 14.54 / Net I/σ(I): 14.54
Reflection shellResolution: 1.27→1.315 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 9185 / CC1/2: 0.471 / CC star: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot0.9.8.7 ELmodel building
PHENIX1.19.2-4158refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→41.26 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.4477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 4657 5 %Random selection
Rwork0.2064 88469 --
obs0.2076 93126 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.27→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 104 452 3269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242916
X-RAY DIFFRACTIONf_angle_d1.23353978
X-RAY DIFFRACTIONf_chiral_restr0.0772487
X-RAY DIFFRACTIONf_plane_restr0.0114513
X-RAY DIFFRACTIONf_dihedral_angle_d14.26821084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.30471520.30052880X-RAY DIFFRACTION98.79
1.28-1.30.27861530.28972905X-RAY DIFFRACTION100
1.3-1.310.29281530.29282919X-RAY DIFFRACTION100
1.31-1.330.28761550.28682935X-RAY DIFFRACTION100
1.33-1.350.30811530.27312917X-RAY DIFFRACTION99.97
1.35-1.370.29161530.27242896X-RAY DIFFRACTION100
1.37-1.390.24991540.26082932X-RAY DIFFRACTION100
1.39-1.410.29941530.25882903X-RAY DIFFRACTION100
1.41-1.430.28891540.25782937X-RAY DIFFRACTION100
1.43-1.450.27171560.24082961X-RAY DIFFRACTION100
1.45-1.480.28771540.23462920X-RAY DIFFRACTION100
1.48-1.50.27171520.2322898X-RAY DIFFRACTION100
1.5-1.530.24881540.21482920X-RAY DIFFRACTION100
1.53-1.560.23371540.21332932X-RAY DIFFRACTION99.97
1.56-1.60.20831540.21612924X-RAY DIFFRACTION100
1.6-1.630.24091570.20032971X-RAY DIFFRACTION100
1.63-1.680.24261550.20972946X-RAY DIFFRACTION100
1.68-1.720.2161540.20542924X-RAY DIFFRACTION99.97
1.72-1.770.23031540.20552925X-RAY DIFFRACTION100
1.77-1.830.20871550.20162949X-RAY DIFFRACTION100
1.83-1.890.23441560.20292968X-RAY DIFFRACTION100
1.89-1.970.2421540.19362934X-RAY DIFFRACTION100
1.97-2.060.22561550.18432942X-RAY DIFFRACTION100
2.06-2.170.20391570.18342972X-RAY DIFFRACTION99.97
2.17-2.30.20091560.1852968X-RAY DIFFRACTION100
2.3-2.480.23371570.1962980X-RAY DIFFRACTION100
2.48-2.730.23891570.20732991X-RAY DIFFRACTION99.84
2.73-3.130.21931590.20193015X-RAY DIFFRACTION99.91
3.13-3.940.1981590.18163026X-RAY DIFFRACTION99.75
3.94-41.260.23391680.21093179X-RAY DIFFRACTION99.61

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