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- PDB-5wa2: Crystal structure of Toxoplasma gondii SAG3 (SRS57) -

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Basic information

Entry
Database: PDB / ID: 5wa2
TitleCrystal structure of Toxoplasma gondii SAG3 (SRS57)
ComponentsSurface antigen
KeywordsMEMBRANE PROTEIN / surface antigen glycoprotein (SAG) / tandem beta-sandwich
Function / homologyProtozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / membrane / Surface antigen
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.591 Å
AuthorsParker, M.L. / Boulanger, M.J.
CitationJournal: To be published
Title: A Toxoplasma lectin-specific activity for sulfated proteoglycans thought to promote infection competency is not dependent on TgSRS57 (TgSAG3)
Authors: Pszenny, V. / Parker, M.L. / Ramaswamy, R. / Grigg, M.E. / Boulanger, M.J.
History
DepositionJun 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 1.2Nov 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 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8952
Polymers33,8031
Non-polymers921
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.130, 59.710, 101.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Surface antigen


Mass: 33802.996 Da / Num. of mol.: 1 / Fragment: UNP residues 38-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: SAG3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BJ39
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→37.472 Å / Num. obs: 40027 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1927 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZQ

1kzq


Resolution: 1.591→37.472 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.13
RfactorNum. reflection% reflection
Rfree0.1912 1950 4.88 %
Rwork0.1693 --
obs0.1704 39961 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 22.9616 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 1.591→37.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 6 325 2513
Biso mean--29.82 31.5 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082268
X-RAY DIFFRACTIONf_angle_d1.2753079
X-RAY DIFFRACTIONf_chiral_restr0.051321
X-RAY DIFFRACTIONf_plane_restr0.007407
X-RAY DIFFRACTIONf_dihedral_angle_d13.793840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.591-1.63080.24471530.219926402793
1.6308-1.67490.23471340.208226692803
1.6749-1.72420.27391440.194826712815
1.7242-1.77980.24781420.190526802822
1.7798-1.84340.23461270.180926962823
1.8434-1.91720.22551460.183626782824
1.9172-2.00450.22691340.168326932827
2.0045-2.11020.16941370.158126992836
2.1102-2.24240.1891410.164426952836
2.2424-2.41550.19141400.160727192859
2.4155-2.65850.1921370.168927182855
2.6585-3.0430.18961310.162827622893
3.043-3.83330.16091300.162127872917
3.8333-37.48250.17311540.16629043058

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