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- PDB-6z7d: Variant Surface Glycoprotein VSGsur mutant H122A soaked in 0.77 m... -

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Basic information

Entry
Database: PDB / ID: 6z7d
TitleVariant Surface Glycoprotein VSGsur mutant H122A soaked in 0.77 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 / plasma membrane / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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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)53,4742
Polymers52,4011
Non-polymers1,0731
Water5,675315
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9484
Polymers104,8022
Non-polymers2,1462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10510 Å2
ΔGint4 kcal/mol
Surface area30840 Å2
Unit cell
Length a, b, c (Å)46.900, 70.950, 130.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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
Components on special symmetry positions
IDModelComponents
11A-910-

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)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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
DManpa1-3DManpa1-6[DManpa1-3]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-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.22 %
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 % 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: 1.75→38.08 Å / Num. obs: 44210 / % possible obs: 98.94 % / Redundancy: 13.3 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 16.67
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 13.8 % / Num. unique obs: 4304 / CC1/2: 0.503 / % possible all: 97.44

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Processing

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

6z79


Resolution: 1.75→38.08 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 4200 5.01 %
Rwork0.178 79619 -
obs0.1792 44206 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.31 Å2 / Biso mean: 39.3723 Å2 / Biso min: 14.13 Å2
Refinement stepCycle: final / Resolution: 1.75→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 72 315 3028
Biso mean--36.81 42.47 -
Num. residues----359
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 (%)
1.75-1.770.37631370.35422608274596
1.77-1.790.28561370.3172626276399
1.79-1.810.31621350.31652652278798
1.81-1.840.35351350.30592619275499
1.84-1.860.3291410.29062611275298
1.86-1.890.29071400.2652659279999
1.89-1.910.28291390.25892604274398
1.91-1.940.26161400.24532682282299
1.94-1.970.27031400.21932642278298
1.97-2.010.23261390.218626412780100
2.01-2.040.24261410.2032686282798
2.04-2.080.19561370.20792612274999
2.08-2.120.23351350.19922674280999
2.12-2.160.24461380.18262610274899
2.16-2.210.21521380.16932664280299
2.21-2.260.17931430.17232666280999
2.26-2.310.22171440.1662640278499
2.31-2.380.2231450.16752668281399
2.38-2.450.19431400.15982681282199
2.45-2.530.22451410.157326282769100
2.53-2.620.1951470.15626972844100
2.62-2.720.18691420.158526712813100
2.72-2.850.20181380.16122626276499
2.85-30.16931360.162626782814100
3-3.180.21051450.165326902835100
3.18-3.430.19381400.157726712811100
3.43-3.770.18281410.156626532794100
3.77-4.320.1911440.142126942838100
4.32-5.440.16121380.156126832821100
5.44-39.120.20311440.193726832827100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46110.370.08021.1213-0.86145.43650.0757-0.2769-0.00440.3043-0.1218-0.08150.03790.24060.07150.1715-0.0021-0.03150.26940.00480.20486.181144.585992.7257
20.54680.0750.1790.96250.15551.32710.0612-0.0698-0.00670.0334-0.0012-0.04990.0161-0.0446-0.04960.0894-0.0035-0.01320.13130.01130.19232.937240.87273.8576
30.8888-0.584-0.85862.35542.24275.58050.05760.2066-0.0081-0.50070.0071-0.15590.15150.21-0.090.31120.03270.05050.19830.00750.20743.523238.118442.8687
40.32560.43040.76370.8961-0.63913.38990.0322-0.26020.11540.4323-0.14220.1107-0.5513-0.16830.14950.35680.01940.03250.3371-0.04430.2566-3.316752.841896.7609
51.32211.4381-0.39443.0879-0.80151.56170.5019-0.3406-0.31091.0906-0.7655-1.0295-0.01880.46530.27260.6269-0.14-0.21110.63470.15650.459613.106236.5897117.6435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 85 )A30 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 197 )A86 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 269 )A198 - 269
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 359 )A270 - 359
5X-RAY DIFFRACTION5chain 'A' and (resid 360 through 411 )A360 - 411

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