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- PDB-6z7a: Variant Surface Glycoprotein VSGsur -

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Basic information

Entry
Database: PDB / ID: 6z7a
TitleVariant Surface Glycoprotein VSGsur
ComponentsVariant surface glycoprotein Sur
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / side of membrane / plasma membrane / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E. / Hashemi, H.
CitationJournal: Nat Microbiol / Year: 2021
Title: A Parasite Coat Protein Binds Suramin to Confer Drug Resistance
Authors: Zeelen, J.P. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Haelg, S. / Wiedemar, N. / Maeser, P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionMay 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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 Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5412
Polymers52,4681
Non-polymers1,0731
Water6,107339
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0824
Polymers104,9362
Non-polymers2,1462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10870 Å2
ΔGint8 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.042, 71.062, 130.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Variant surface glycoprotein Sur


Mass: 52468.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: VSGsur / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A291L8F4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19-24 % PEG 400 100 mM TEA/HCl pH=7.5 10 % (v/v) Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.21→48.05 Å / Num. obs: 122573 / % possible obs: 91.43 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09566 / Rpim(I) all: 0.04114 / Rrim(I) all: 0.1044 / Net I/σ(I): 8.57
Reflection shellResolution: 1.21→1.25 Å / Num. unique obs: 7073 / CC1/2: 0.174

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Processing

Software
NameVersionClassification
AutoProcessdata collection
PHENIX1.17.1_3660refinement
Cootmodel building
pointlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z79

6z79


Resolution: 1.21→48.05 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 6192 5.05 %
Rwork0.1659 116381 -
obs0.1669 122545 91.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.66 Å2
Refinement stepCycle: LAST / Resolution: 1.21→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 72 339 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01932864
X-RAY DIFFRACTIONf_angle_d1.54073927
X-RAY DIFFRACTIONf_chiral_restr0.2389479
X-RAY DIFFRACTIONf_plane_restr0.0116510
X-RAY DIFFRACTIONf_dihedral_angle_d15.08991072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.39771080.38911960X-RAY DIFFRACTION47.11
1.22-1.240.40431140.3742234X-RAY DIFFRACTION52.27
1.24-1.250.37321380.3752485X-RAY DIFFRACTION59.78
1.25-1.270.3591670.35952756X-RAY DIFFRACTION65.97
1.27-1.290.32841570.34793071X-RAY DIFFRACTION73.46
1.29-1.30.36631710.32853378X-RAY DIFFRACTION80.42
1.3-1.320.30021870.32863609X-RAY DIFFRACTION85.73
1.32-1.340.2972130.30513889X-RAY DIFFRACTION92.2
1.34-1.360.30842200.30434040X-RAY DIFFRACTION96.88
1.36-1.380.29592320.27474165X-RAY DIFFRACTION99.08
1.38-1.410.26212040.24244157X-RAY DIFFRACTION99.52
1.41-1.430.22642200.2284214X-RAY DIFFRACTION99.46
1.43-1.460.24962510.21384189X-RAY DIFFRACTION99.57
1.46-1.490.19962390.18674157X-RAY DIFFRACTION99.5
1.49-1.520.19062240.18054194X-RAY DIFFRACTION99.35
1.52-1.560.1942020.1684191X-RAY DIFFRACTION98.72
1.56-1.60.16592170.15354187X-RAY DIFFRACTION99.46
1.6-1.640.18082350.14754203X-RAY DIFFRACTION99.35
1.64-1.690.15862390.13214220X-RAY DIFFRACTION99.82
1.69-1.740.13762160.12254211X-RAY DIFFRACTION99.46
1.74-1.810.14552350.12034213X-RAY DIFFRACTION99.53
1.81-1.880.12322280.12094197X-RAY DIFFRACTION98.95
1.88-1.960.14892510.11764207X-RAY DIFFRACTION99.62
1.96-2.070.12372110.12164249X-RAY DIFFRACTION99.64
2.07-2.20.13662130.11864264X-RAY DIFFRACTION99.84
2.2-2.370.16552180.12354264X-RAY DIFFRACTION98.74
2.37-2.610.16712240.13314271X-RAY DIFFRACTION99.56
2.61-2.980.17612210.15044311X-RAY DIFFRACTION99.52
2.98-3.760.17682080.16724347X-RAY DIFFRACTION98.96
3.76-48.050.21242290.18774548X-RAY DIFFRACTION99.07

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