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- PDB-6z79: Variant Surface Glycoprotein VSGsur, I3C ("Magic Triangle") deriv... -

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Basic information

Entry
Database: PDB / ID: 6z79
TitleVariant Surface Glycoprotein VSGsur, I3C ("Magic Triangle") derivative used for phasing of the structure and subsequently as a model for molecular replacement of native, mutants, and drug soaks.
ComponentsVariant surface glycoprotein Sur
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation Magic Triangle I3C
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / side of membrane / plasma membrane / Chem-I3C / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 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 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)53,9383
Polymers52,4681
Non-polymers1,4702
Water4,017223
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8756
Polymers104,9362
Non-polymers2,9394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10130 Å2
ΔGint4 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.955, 70.893, 129.652
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-(1-3)-[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: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H4I3NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
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: 14.2 / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 3, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 1.92→44.15 Å / Num. obs: 27999 / % possible obs: 82.57 % / Redundancy: 18.1 % / Biso Wilson estimate: 30.05 Å2 / CC1/2: 0.995 / Net I/σ(I): 13.99
Reflection shellResolution: 1.92→1.989 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 845 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata processing
Cootmodel building
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→44.15 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1124 4.02 %
Rwork0.2343 26869 -
obs0.235 27993 82.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.05 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 77 223 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782604
X-RAY DIFFRACTIONf_angle_d0.9943550
X-RAY DIFFRACTIONf_chiral_restr0.0644430
X-RAY DIFFRACTIONf_plane_restr0.0061464
X-RAY DIFFRACTIONf_dihedral_angle_d17.1136952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.010.3822470.33061120X-RAY DIFFRACTION28.2
2.01-2.110.28651000.29292405X-RAY DIFFRACTION59.81
2.11-2.250.27771500.23973573X-RAY DIFFRACTION88.79
2.25-2.420.25271570.23833765X-RAY DIFFRACTION93.78
2.42-2.660.23091610.23973841X-RAY DIFFRACTION95.1
2.66-3.050.28471630.24163912X-RAY DIFFRACTION96.38
3.05-3.840.23871680.2114008X-RAY DIFFRACTION97.34
3.84-44.150.24431780.23534245X-RAY DIFFRACTION98.6
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)
11.385699351220.132950763530.3496494152631.06520629552-0.08824896571183.558866169280.101471470477-0.6000287706030.01208800362710.443289694981-0.02437829169110.00262931284572-0.0242092416918-0.1250553189340.001447750601350.257226306448-0.0169845074541-0.003019699704550.365627513905-0.01880177797480.1496068983432.7337290219343.393170975791.9185001263
21.249941249110.4336608580542.136996759211.781845807281.947752585036.502888503850.008169984401590.237233765049-0.121228751702-0.4789369283940.109593042073-0.0506529372383-0.04130481910270.0481524531379-0.1117588023340.361749845799-0.0425305526890.04599107386560.2639940360050.0126123715670.1990061490823.2975032153131.717607845943.899518314
32.67254530695-2.05763896442-2.365553909935.22118030601-0.06658741723395.149338695030.453267899193-1.100823315280.8381077855940.328120934225-0.151167704357-0.604900678948-0.5082702399720.457424096094-0.2902745084420.331177548809-0.160326880940.0165133346540.431825574182-0.1232551651820.35137560173811.110953243954.259766242178.3403758351
41.1255391506-0.436016341538-1.247345845532.417119325492.696050580517.46093465990.04706195098940.1956867673870.0913515688451-0.5809548426740.151730851795-0.16855240636-0.2116511250340.332079529619-0.1623004333910.2891934678360.01294133439060.02788857488010.2310973048090.04050795840610.1866718177113.4009238646538.423826467143.0088959551
56.00651618986-0.4373259898622.304562176381.98158847584-2.834189862714.54289694327-0.0480116830795-0.4732026233080.4172195822930.3419310770140.07840774205870.215837783628-0.312016899834-0.3752134105290.006460671143350.2205848114340.03717439091220.06176573134020.249041219103-0.0232870515150.239466237527-10.395885890253.341334189776.5446387878
60.1967422908180.4926987922950.4003622578011.254077877441.070081156390.8707328089960.407336950427-0.3384293262520.3120099284240.78139602864-0.1614980398590.15644631841-0.604361073010.351429941309-0.173972377030.897645372971-0.178791871038-0.0011198978920.969868222298-0.009474194168330.258958962126.3121642404952.219447558114.225829253
73.006842080550.517862126060.4593481160289.6701735229-1.166605566910.7789715071510.515373167574-0.0955750093935-0.2802047440730.341644208659-0.796617947512-0.304074899211-0.06063022419120.7370157390570.4247623326810.8387690046-0.149936333642-0.1073671784610.8962201615340.2447027661110.49932625724611.699267429331.7724097127115.2437748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 269 )
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 370 )
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 409 )

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