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- PDB-6y0d: Crystal structure of Trypanosoma cruzi antigen TcSMP11.90 -

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Basic information

Entry
Database: PDB / ID: 6y0d
TitleCrystal structure of Trypanosoma cruzi antigen TcSMP11.90
ComponentsSurface membrane protein
KeywordsIMMUNE SYSTEM / Trypanosoma cruzi / antigen / Chagas
Function / homologymembrane / Surface membrane protein
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDi Pisa, F. / Gourlay, L.J. / Bolognesi, M. / De Benedetti, S.
CitationJournal: Vaccines (Basel) / Year: 2022
Title: Elucidating the 3D Structure of a Surface Membrane Antigen from Trypanosoma cruzi as a Serodiagnostic Biomarker of Chagas Disease.
Authors: Di Pisa, F. / De Benedetti, S. / Fassi, E.M.A. / Bombaci, M. / Grifantini, R. / Musico, A. / Frigerio, R. / Pontillo, A. / Rigo, C. / Abelli, S. / Grande, R. / Zanchetta, N. / Mileto, D. / ...Authors: Di Pisa, F. / De Benedetti, S. / Fassi, E.M.A. / Bombaci, M. / Grifantini, R. / Musico, A. / Frigerio, R. / Pontillo, A. / Rigo, C. / Abelli, S. / Grande, R. / Zanchetta, N. / Mileto, D. / Mancon, A. / Rizzo, A. / Gori, A. / Cretich, M. / Colombo, G. / Bolognesi, M. / Gourlay, L.J.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface membrane protein


Theoretical massNumber of molelcules
Total (without water)43,4061
Polymers43,4061
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.890, 33.192, 67.445
Angle α, β, γ (deg.)90.000, 108.059, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-551-

HOH

31A-643-

HOH

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Components

#1: Protein Surface membrane protein


Mass: 43406.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_40g219 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2WZ57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG buffer pH 5, 20% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→64.12 Å / Num. obs: 26050 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.62→1.71 Å / Num. unique obs: 3749 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLH

5klh


Resolution: 1.62→44.18 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6984
RfactorNum. reflection% reflection
Rfree0.2293 1258 4.91 %
Rwork0.1922 --
obs0.1941 25643 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.66 Å2
Refinement stepCycle: LAST / Resolution: 1.62→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 0 161 1765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871681
X-RAY DIFFRACTIONf_angle_d0.95312305
X-RAY DIFFRACTIONf_chiral_restr0.0603269
X-RAY DIFFRACTIONf_plane_restr0.0056305
X-RAY DIFFRACTIONf_dihedral_angle_d16.1136623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.34421380.30882716X-RAY DIFFRACTION99.27
1.68-1.760.30281290.25912725X-RAY DIFFRACTION99.86
1.76-1.850.2451460.22522728X-RAY DIFFRACTION99.9
1.85-1.970.37611230.28772518X-RAY DIFFRACTION91.48
1.97-2.120.21921370.19762737X-RAY DIFFRACTION99.83
2.12-2.340.27891320.23462606X-RAY DIFFRACTION95.14
2.34-2.670.22141380.19972762X-RAY DIFFRACTION99.93
2.67-3.370.2371630.18852748X-RAY DIFFRACTION99.93

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