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- PDB-2jks: Crystal structure of the the bradyzoite specific antigen BSR4 fro... -

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Basic information

Entry
Database: PDB / ID: 2jks
TitleCrystal structure of the the bradyzoite specific antigen BSR4 from toxoplasma gondii.
ComponentsBRADYZOITE SURFACE ANTIGEN BSR4
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Bradyzoite surface antigen BSR4
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBoulanger, M.J. / Grigg, M.E. / Bruic, E. / Grujic, O.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Characterization of the Bradyzoite Surface Antigen (Bsr4) from Toxoplasma Gondii, a Unique Addition to the Surface Antigen Glycoprotein 1-Related Superfamily.
Authors: Crawford, J. / Grujic, O. / Bruic, E. / Czjzek, M. / Grigg, M.E. / Boulanger, M.J.
History
DepositionAug 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRADYZOITE SURFACE ANTIGEN BSR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5859
Polymers34,0621
Non-polymers5238
Water5,026279
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.050, 92.050, 98.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BRADYZOITE SURFACE ANTIGEN BSR4 / BSR4


Mass: 34061.887 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: ME49 / Plasmid: PACGP67B / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): HI5 / References: UniProt: Q95NL6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.58 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 10, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.6 Å / Num. obs: 396248 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 11.69 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11.41 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KZQ

1kzq


Resolution: 1.9→30.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.914 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1715 5.1 %RANDOM
Rwork0.238 ---
obs0.24 32104 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 8 279 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.9442965
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2335279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.06525.81486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.523157
X-RAY DIFFRACTIONr_chiral_restr0.1490.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021593
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.2990
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21432
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2291.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10322300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9373813
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4754.5665
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 130
Rwork0.334 2312
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)
11.22611.1084-1.36131.3225-0.43093.50610.2450.13920.37060.09220.05750.2923-0.028-0.0269-0.3025-0.0382-0.00270.1083-0.03830.0270.0474-2.913213.384224.9614
21.94251.12720.70471.01320.04320.6280.1585-0.42350.16160.735-0.0699-0.17470.12460.4951-0.08850.12440.00420.03760.03250.0062-0.14147.82439.060135.4229
30.14920.1495-0.32190.61360.16371.20440.1411-0.08040.07030.0982-0.12480.06740.06150.1708-0.01630.0135-0.01650.0592-0.02410.0015-0.0254.876111.793525.9358
41.2497-0.3691-1.01431.3965-0.97063.3065-0.005-0.0140.05430.08640.0632-0.0103-0.15970.0597-0.0581-0.01270.0065-0.0139-0.04-0.0099-0.034826.53273.77710.9306
50.22780.0137-0.71650.5178-0.5012.6596-0.0286-0.05780.045-0.01050.09170.03960.06560.0382-0.0631-0.01210.0307-0.0045-0.0317-0.0084-0.024629.1875-1.0955-0.0431
60.3059-0.133-0.37721.27420.40490.51290.003-0.05720.15770.02210.0709-0.09530.0876-0.0523-0.0738-0.06180.0219-0.00630.0235-0.0338-0.005526.29089.0678-2.1989
70.6802-0.0772-0.68280.28560.25280.79640.0023-0.05110.04060.03140.04480.01420.04830.0919-0.0471-0.03090.01730.005-0.01560.0171-0.039418.57455.440710.8196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 10
2X-RAY DIFFRACTION1A13 - 18
3X-RAY DIFFRACTION1A30 - 35
4X-RAY DIFFRACTION1A40 - 48
5X-RAY DIFFRACTION2A53 - 57
6X-RAY DIFFRACTION2A65 - 67
7X-RAY DIFFRACTION2A76 - 79
8X-RAY DIFFRACTION2A83 - 89
9X-RAY DIFFRACTION3A116 - 121
10X-RAY DIFFRACTION3A132 - 141
11X-RAY DIFFRACTION3A152 - 161
12X-RAY DIFFRACTION3A167 - 169
13X-RAY DIFFRACTION4A172 - 176
14X-RAY DIFFRACTION4A187 - 191
15X-RAY DIFFRACTION4A197 - 201
16X-RAY DIFFRACTION4A206 - 209
17X-RAY DIFFRACTION5A254 - 258
18X-RAY DIFFRACTION5A269 - 277
19X-RAY DIFFRACTION6A1316 - 1323
20X-RAY DIFFRACTION7A2001 - 2279

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