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- PDB-2y8t: Co-structure of AMA1 with a surface exposed region of RON2 from T... -

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Basic information

Entry
Database: PDB / ID: 2y8t
TitleCo-structure of AMA1 with a surface exposed region of RON2 from Toxoplasma gondii
Components
  • APICAL MEMBRANE ANTIGEN, PUTATIVE
  • RHOPTRY NECK PROTEIN 2
KeywordsMEMBRANE PROTEIN / MOVING JUNCTION / INVASION
Function / homology
Function and homology information


host cell plasma membrane / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Complement Module; domain 1 - #70 / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Complement Module; domain 1 / 3-Layer(bba) Sandwich / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / Apical membrane antigen 1 / Rhoptry neck protein 2 / Apical membrane antigen 1 / :
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J.
CitationJournal: Science / Year: 2011
Title: Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of Ama1 with a Ron2 Peptide
Authors: Tonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J.
History
DepositionFeb 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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

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Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
B: RHOPTRY NECK PROTEIN 2
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
E: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0988
Polymers103,5324
Non-polymers5664
Water10,881604
1
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
B: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9873
Polymers51,7662
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-21.8 kcal/mol
Surface area18470 Å2
MethodPISA
2
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
E: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1115
Polymers51,7662
Non-polymers3453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-22.1 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.860, 96.380, 78.350
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APICAL MEMBRANE ANTIGEN, PUTATIVE / AMA1 / APICAL MEMBRANE ANTIGEN 1


Mass: 48013.457 Da / Num. of mol.: 2 / Fragment: DOMAINS I/II/III, RESIDUES 64-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B9QC59, UniProt: B6KAM0*PLUS
#2: Protein/peptide RHOPTRY NECK PROTEIN 2 / RON2


Mass: 3752.296 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-271 / Source method: obtained synthetically / Source: (synth.) TOXOPLASMA GONDII (eukaryote) / References: UniProt: B9QQC1, UniProt: B6KV60*PLUS
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMIDATED THREONINE (9AT): AMIDATED C-TERMINAL THREONINE
Sequence detailsFOR CHAINS B AND E AUTHOR HAS PROVIDED A GENBANK REFERENCE HQ110093.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.57 % / Description: NONE
Crystal growDetails: 25% PEG 1500, 100 MM MIB PH 4.0 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→45 Å / Num. obs: 68179 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2Z

2x2z


Resolution: 1.95→39.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.347 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22804 3453 5.1 %RANDOM
Rwork0.17013 ---
obs0.173 64686 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.694 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 36 604 7312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9589394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63824.8325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.542151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3341533
X-RAY DIFFRACTIONr_chiral_restr0.2130.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215349
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_it1.4691.54278
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54926919
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.91132639
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0924.52472
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 251 -
Rwork0.207 4741 -
obs--99.72 %

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