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- PDB-8ddp: Crystal structure of SRS57 from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 8ddp
TitleCrystal structure of SRS57 from Toxoplasma gondii
ComponentsSAG-related sequence SRS57
KeywordsMEMBRANE PROTEIN / Surface Antigen Glycoprotein / SAG / Related Sequences / SRS
Function / homologyProtozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / membrane / SAG-related sequence SRS57
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsRamaswamy, R. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structure of SRS29C from Toxoplasma gondii
Authors: Ramaswamy, R. / Boulanger, M.J.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAG-related sequence SRS57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3182
Polymers31,2261
Non-polymers921
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, eluted as a monomer in size exclusion chromatography
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 SAG-related sequence SRS57


Mass: 31226.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: SRS57, TGME49_308020 / Plasmid: pAcGP67b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A125YY85
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→43.48 Å / Num. obs: 40027 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 1927

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZQ

1kzq


Resolution: 1.591→37.472 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 1950 4.88 %
Rwork0.1693 38011 -
obs0.1704 39961 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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 / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.591-1.63080.24471530.21992640
1.6308-1.67490.23471340.20822669
1.6749-1.72420.27391440.19482671
1.7242-1.77980.24781420.19052680
1.7798-1.84340.23461270.18092696
1.8434-1.91720.22551460.18362678
1.9172-2.00450.22691340.16832693
2.0045-2.11020.16941370.15812699
2.1102-2.24240.1891410.16442695
2.2424-2.41550.19141400.16072719
2.4155-2.65850.1921370.16892718
2.6585-3.0430.18961310.16282762
3.043-3.83330.16091300.16212787

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