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- PDB-6z7e: Variant Surface Glycoprotein VSGsur mutant H122A soaked in 7.7 mM... -

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Basic information

Entry
Database: PDB / ID: 6z7e
TitleVariant Surface Glycoprotein VSGsur mutant H122A soaked in 7.7 mM suramin
ComponentsVariant surface glycoprotein Sur
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation VSG
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: 1.663 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E.
CitationJournal: Nat Microbiol / Year: 2021
Title: Structure of trypanosome coat protein VSGsur and function in suramin resistance.
Authors: Zeelen, J. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Halg, S. / Wiedemar, N. / Maser, P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionMay 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 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 1.2Oct 16, 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)53,3122
Polymers52,4011
Non-polymers9111
Water5,098283
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6244
Polymers104,8022
Non-polymers1,8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10050 Å2
ΔGint-6 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.936, 71.033, 130.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-844-

HOH

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Components

#1: Protein Variant surface glycoprotein Sur


Mass: 52401.016 Da / Num. of mol.: 1 / Mutation: H122A
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-(1-3)-[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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 40.8 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.663→39.16 Å / Num. obs: 52136 / % possible obs: 99.79 % / Redundancy: 13.2 % / CC1/2: 1 / Net I/σ(I): 19.44
Reflection shellResolution: 1.663→1.723 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5028 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z79

6z79


Resolution: 1.663→39.16 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 4941 4.99 %
Rwork0.1845 94024 -
obs0.1857 52131 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.29 Å2 / Biso mean: 39.0156 Å2 / Biso min: 13.14 Å2
Refinement stepCycle: final / Resolution: 1.663→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 61 283 2953
Biso mean--30 41.27 -
Num. residues----356
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 (%)
1.66-1.680.32131560.30932973312994
1.68-1.70.32961630.303631003263100
1.7-1.720.30971610.292631403301100
1.72-1.740.341660.289431943360100
1.74-1.770.2671590.286130973256100
1.77-1.790.27511590.266231753334100
1.79-1.820.27681640.255931643328100
1.82-1.840.31171640.249430993263100
1.84-1.870.271640.22931833347100
1.87-1.90.23461670.223531073274100
1.9-1.940.2521730.209231443317100
1.94-1.970.20951620.1931473309100
1.97-2.010.20341630.197730923255100
2.01-2.050.21511660.177431873353100
2.05-2.10.19891640.184931173281100
2.1-2.140.18721690.180131523321100
2.14-2.20.19361660.163531533319100
2.2-2.260.18591640.161531393303100
2.26-2.320.20621670.166131193286100
2.32-2.40.25151640.168631363300100
2.4-2.480.18991680.164231463314100
2.48-2.580.16091660.168731323298100
2.58-2.70.21621630.167331333296100
2.7-2.840.2421700.177531503320100
2.84-3.020.19431650.18231333298100
3.02-3.250.16971690.177531573326100
3.26-3.580.19721700.170931363306100
3.58-4.10.19231630.156531353298100
4.1-5.160.15851630.160331323295100
5.17-44.170.24421630.207531523315100

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