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- PDB-1ynt: Structure of the monomeric form of T. gondii SAG1 surface antigen... -

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Basic information

Entry
Database: PDB / ID: 1ynt
TitleStructure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab
Components
  • 4F11E12 Fab variable heavy chain region
  • 4F11E12 Fab variable light chain region
  • Major surface antigen p30
  • protein L
KeywordsIMMUNE SYSTEM / Toxoplasma gondii / recombinant SAG1 / conformational epitope
Function / homology
Function and homology information


symbiont-containing vacuole / IgG binding / immunoglobulin binding / membrane
Similarity search - Function
SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding ...SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Major surface antigen p30 / Protein L
Similarity search - Component
Biological speciesFinegoldia magna (bacteria)
Toxoplasma gondii (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGraille, M. / Stura, E.A. / Bossus, M. / Muller, B.H. / Letourneur, O. / Battail-Poirot, N. / Sibai, G. / Rolland, D. / Le Du, M.H. / Ducancel, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response
Authors: Graille, M. / Stura, E.A. / Bossus, M. / Muller, B.H. / Letourneur, O. / Battail-Poirot, N. / Sibai, G. / Gauthier, M. / Rolland, D. / Le Du, M.H. / Ducancel, F.
History
DepositionJan 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 3, 2018Group: Structure summary / Category: audit_author / struct / Item: _audit_author.name / _struct.title
Revision 1.5Dec 4, 2019Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4F11E12 Fab variable light chain region
B: 4F11E12 Fab variable heavy chain region
C: 4F11E12 Fab variable light chain region
D: 4F11E12 Fab variable heavy chain region
E: protein L
F: Major surface antigen p30
G: Major surface antigen p30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5489
Polymers154,3237
Non-polymers2252
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.034, 198.285, 128.366
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a Fab - antigen complex. Two are present in the asymetric unit

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Components

#1: Antibody 4F11E12 Fab variable light chain region


Mass: 23577.820 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody 4F11E12 Fab variable heavy chain region


Mass: 23568.344 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein protein L


Mass: 6750.485 Da / Num. of mol.: 1 / Fragment: domain C*
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: Q51918*PLUS
#4: Protein Major surface antigen p30 / SAG1 protein


Mass: 26640.217 Da / Num. of mol.: 2 / Fragment: residues in database 50-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pTG8639 / Production host: Pichia pastoris (fungus) / References: UniProt: P13664
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
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: 2.8 Å3/Da / Density % sol: 57.985123 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 11
Details: 15% polyethylene glycol 3350, 0.25M NaCl, 150mM CAPS, pH 11, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 29, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 32176 / Num. obs: 31886 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Χ2: 1.241
Reflection shellResolution: 3.1→3.19 Å / Rmerge(I) obs: 0.497 / Num. unique all: 2608 / Χ2: 0.866 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.501data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB codes: 1F11, 1KB5, 1KZQ

1f11

1kb5

1kzq


Resolution: 3.1→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.283 1534 4.8 %
Rwork0.241 --
all-30981 -
obs-30981 96.7 %
Displacement parametersBiso mean: 10 Å2
Baniso -1Baniso -2Baniso -3
1--11.613 Å20 Å20 Å2
2---9.251 Å20 Å2
3---20.864 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 2 0 10802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.535

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