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- PDB-4yiv: Crystal structure of engineered TgAMA1 lacking the DII loop -

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Basic information

Entry
Database: PDB / ID: 4yiv
TitleCrystal structure of engineered TgAMA1 lacking the DII loop
ComponentsApical membrane antigen AMA1
KeywordsIMMUNE SYSTEM / Apicomplexa / invasion / moving junction / parasite / protein engineering / PAN domain
Function / homology
Function and homology information


Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / Apical membrane antigen AMA1
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsParker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP82915 Canada
CitationJournal: Plos One / Year: 2015
Title: An Extended Surface Loop on Toxoplasma gondii Apical Membrane Antigen 1 (AMA1) Governs Ligand Binding Selectivity.
Authors: Parker, M.L. / Boulanger, M.J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apical membrane antigen AMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94211
Polymers46,0641
Non-polymers87810
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.050, 89.050, 124.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-658-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Apical membrane antigen AMA1


Mass: 46064.297 Da / Num. of mol.: 1 / Fragment: residues 64-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_255260 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: S8GKS3
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 242 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe authors state that twenty residues of the DII loop (HTYPLTSQASWNDWWPLHQS) were replaced with a ...The authors state that twenty residues of the DII loop (HTYPLTSQASWNDWWPLHQS) were replaced with a Gly-Ser linker (GSGSGSG).

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mM cobalt (II) chloride hexahydrate, 5 mM nickel (II) chloride hexahydrate, 5 mM cadmium chloride hydrate, 5 mM magnesium chloride hexahydrate, 0.1 M Hepes pH 7.5, 12% PEG 3350, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→56.24 Å / Num. all: 38493 / Num. obs: 38493 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.8
Reflection shellResolution: 1.93→2.11 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4 / % possible all: 91.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y8T

2y8t


Resolution: 1.93→39.824 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1920 5 %Random selection
Rwork0.1762 36465 --
obs0.1771 38385 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.35 Å2 / Biso mean: 36.4114 Å2 / Biso min: 15.25 Å2
Refinement stepCycle: final / Resolution: 1.93→39.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 19 233 3181
Biso mean--41.65 38.65 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123042
X-RAY DIFFRACTIONf_angle_d1.3564110
X-RAY DIFFRACTIONf_chiral_restr0.055432
X-RAY DIFFRACTIONf_plane_restr0.007540
X-RAY DIFFRACTIONf_dihedral_angle_d14.351129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9301-1.97840.26271280.21512547267599
1.9784-2.03180.24411460.202925402686100
2.0318-2.09160.22231250.192825592684100
2.0916-2.15910.22751280.186725762704100
2.1591-2.23630.24021490.184725602709100
2.2363-2.32580.21371400.175925702710100
2.3258-2.43170.21071230.168225872710100
2.4317-2.55980.20611410.169525872728100
2.5598-2.72020.20771470.174525772724100
2.7202-2.93020.21091250.170626092734100
2.9302-3.22490.17991640.167325942758100
3.2249-3.69130.181390.168126512790100
3.6913-4.64950.17511400.155426702810100
4.6495-39.83280.17611250.198328382963100

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