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- PDB-2wnk: Structure of SporoSAG from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 2wnk
TitleStructure of SporoSAG from Toxoplasma gondii
ComponentsSPOROZOITE-SPECIFIC SAG PROTEIN
KeywordsMEMBRANE PROTEIN
Function / homologySRS domain / SRS domain / SRS domain / SRS domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / membrane / Sporozoite-specific SAG protein
Function and homology information
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.55 Å
AuthorsCrawford, J. / Lamb, E. / Grujic, O. / Grigg, M.E. / Boulanger, M.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and Functional Characterization of Sporosag: A Sag2 Related Surface Antigen from Toxoplasma Gondii.
Authors: Crawford, J. / Lamb, E. / Wasmuth, J. / Grujic, O. / Grigg, M.E. / Boulanger, M.J.
History
DepositionJul 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPOROZOITE-SPECIFIC SAG PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,8541
Polymers24,8541
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.496, 106.496, 31.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-2097-

HOH

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Components

#1: Protein SPOROZOITE-SPECIFIC SAG PROTEIN / SPOROSAG


Mass: 24853.820 Da / Num. of mol.: 1 / Fragment: RESIDUES, 27-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Cell line (production host): High Five / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q6RUA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.91 Å3/Da / Density % sol: 35.18 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Date: Jun 6, 2008 / Details: OSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→30.7 Å / Num. obs: 30054 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 52.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
iMOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.55→23.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.716 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24589 1519 5.1 %RANDOM
Rwork0.20172 ---
obs0.20395 28535 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.55→23.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 0 310 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9662241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg25.2855220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.35826.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91615273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.392154
X-RAY DIFFRACTIONr_chiral_restr0.1670.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211205
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0621.51109
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78821783
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8813539
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8444.5458
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 104 -
Rwork0.392 1993 -
obs--95.36 %
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)
11.9612-0.66390.25424.4146-0.31620.59330.10010.04-0.229-0.09480.07410.15870.1025-0.025-0.17420.0654-0.0071-0.05690.0291-0.01560.1863-50.806413.75569.9089
21.42390.13910.64031.55160.56681.410.0157-0.0088-0.04540.0332-0.06060.08480.06-0.00870.04490.1147-0.01170.00870.1078-0.00170.0044-26.5934-2.91631.0054
30.7858-0.48470.49490.8501-0.5220.61340.05930.0104-0.0389-0.0094-0.02290.16950.01810.0651-0.03650.088-0.01830.00040.0722-0.01790.0615-37.08715.14522.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 130
2X-RAY DIFFRACTION2A131 - 238
3X-RAY DIFFRACTION3A2001 - 2310

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