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- PDB-8q0e: Crystal Structure of the N-terminal Domain of Variant Surface Gly... -

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Basic information

Entry
Database: PDB / ID: 8q0e
TitleCrystal Structure of the N-terminal Domain of Variant Surface Glycoprotein 545 (VSG545) of Trypanosome brucei brucei Lister 427
ComponentsVariant surface glycoprotein 545
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Glycosylation MEMBRANE PROTEIN
Function / homologyTrypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response / plasma membrane / Variant surface glycoprotein 545
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
Authorsvan Straaten, M. / Stebbins, C.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
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
DepositionJul 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein 545
B: Variant surface glycoprotein 545


Theoretical massNumber of molelcules
Total (without water)102,7982
Polymers102,7982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-63 kcal/mol
Surface area20810 Å2
Unit cell
Length a, b, c (Å)46.414, 52.284, 305.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Variant surface glycoprotein 545


Mass: 51398.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: M4SXB0

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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

Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5 / Details: 100 mM MES/NaOH 22 % PEG 8000 and 300 mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→46.52 Å / Num. obs: 13575 / % possible obs: 75.58 % / Redundancy: 4.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.2451 / Net I/σ(I): 5.63
Reflection shellResolution: 3.15→3.26 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 619 / CC1/2: 0.785 / % possible all: 45.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
pointlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.52 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 536 5.17 %
Rwork0.2358 --
obs0.2385 10364 75.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 0 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033487
X-RAY DIFFRACTIONf_angle_d0.5334731
X-RAY DIFFRACTIONf_dihedral_angle_d4.119486
X-RAY DIFFRACTIONf_chiral_restr0.039589
X-RAY DIFFRACTIONf_plane_restr0.005616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.460.3578890.30661565X-RAY DIFFRACTION50
3.46-3.960.35281030.24322129X-RAY DIFFRACTION66
3.96-4.990.25451550.2082769X-RAY DIFFRACTION86
4.99-46.520.2621890.23663365X-RAY DIFFRACTION98
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)
10.2-0.20050.05440.5746-0.22060.4566-0.0426-0.0521-0.04640.23250.086-0.0632-0.0003-0.08390.05720.0568-0.0368-0.14550.37160.3040.27932.4627.383923.9228
20.15890.057-0.10890.5930.06680.8623-0.0454-0.02850.02790.3906-0.04470.03870.1184-0.0028-0.070.0466-0.10440.02820.18620.19310.20939.21319.834626.2387
30.1820.082-0.08251.4902-1.42991.3695-0.068-0.1464-0.2874-0.06660.0029-0.00390.54810.0575-0.03070.7439-0.07930.03090.56890.16650.25457.619-15.552275.4801
40.28040.055-0.05526.9901-0.02890.05550.01650.15620.1759-0.4721-0.02470.5903-0.2128-0.7284-0.04640.4763-0.0376-0.0741.00520.14010.28360.8867-8.76151.1752
50.0930.3486-0.13771.9748-1.87352.97390.2371-0.3055-0.00540.42660.12460.3166-0.1221-0.7867-0.27080.5710.0693-0.00650.74190.15770.24551.9298-6.107176.8614
63.09280.7852-0.7296.4391-6.71927.01040.1837-0.07350.73630.8406-0.2174-0.0768-1.59440.0073-0.01391.0816-0.06620.10830.3754-0.00060.36497.303412.341653.7289
71.70210.19630.74830.03280.28466.0325-0.04580.14730.1863-0.0554-0.2050.1429-0.6014-0.35960.36080.8509-0.0542-0.26130.26970.03040.33199.451214.142336.7214
81.19580.3416-0.6720.52460.02330.4981-0.0416-0.3095-0.28160.2677-0.1859-0.16970.15070.2745-0.0248-0.0222-0.01660.03350.40030.13050.237320.63334.344923.56
90.28260.0523-0.00310.528-0.05760.0019-0.0222-0.0905-0.10540.4801-0.123-0.0671-0.02760.1336-0.37260.1971-0.0553-0.17030.29460.23140.111513.5516-0.309944.0373
101.7320.4140.31741.51260.81993.6552-0.1308-0.1871-0.2892-0.0441-0.1207-0.36890.07160.60670.19060.65090.0725-0.03440.31620.03820.302619.4443-8.075366.2716
110.5715-0.33120.32361.4071-1.36982.03970.0252-0.0731-0.2543-0.2441-0.135-0.19940.72750.2181-0.0590.78410.0054-0.02930.53110.22840.316916.2183-13.654862.8649
120.65840.09710.08380.9481-0.23581.5233-0.02430.14290.0322-0.1395-0.0274-0.1550.01190.07860.15390.548-0.0260.06980.28590.29350.298613.1553-8.189730.3147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 242 )
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 163 )
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 221 )
11X-RAY DIFFRACTION11chain 'B' and (resid 222 through 272 )
12X-RAY DIFFRACTION12chain 'B' and (resid 273 through 298 )

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