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- PDB-2y8r: Crystal structure of apo AMA1 mutant (Tyr230Ala) from Toxoplasma ... -

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Basic information

Entry
Database: PDB / ID: 2y8r
TitleCrystal structure of apo AMA1 mutant (Tyr230Ala) from Toxoplasma gondii
ComponentsAPICAL MEMBRANE ANTIGEN, PUTATIVE
KeywordsMEMBRANE PROTEIN / MOVING JUNCTION / INVASION
Function / homology
Function and homology information


extracellular region / plasma membrane
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
Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
B: APICAL MEMBRANE ANTIGEN, PUTATIVE
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
E: APICAL MEMBRANE ANTIGEN, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,5708
Polymers191,6854
Non-polymers8854
Water9,530529
1
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1432
Polymers47,9211
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APICAL MEMBRANE ANTIGEN, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1432
Polymers47,9211
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1432
Polymers47,9211
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: APICAL MEMBRANE ANTIGEN, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1432
Polymers47,9211
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.520, 76.090, 88.780
Angle α, β, γ (deg.)71.89, 73.37, 73.50
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 47921.363 Da / Num. of mol.: 4 / Fragment: DOMAINS I/II/III, RESIDUES 64-484 / Mutation: YES
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: 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.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 230 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN D, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN E, TYR 230 TO ALA
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.89 % / Description: NONE
Crystal growDetails: 21% PEG3350, 100 MM TRIS PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795
DetectorType: MARMOSAIC 325 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: 2.35→38.59 Å / Num. obs: 63415 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→38.59 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.839 / SU B: 13.133 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 2.724 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30493 2834 5.1 %RANDOM
Rwork0.2116 ---
obs0.21635 53192 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.03 Å2-0.02 Å2
2--0 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12567 0 56 529 13152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.95117670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36151586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30224.665626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.411152092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4251562
X-RAY DIFFRACTIONr_chiral_restr0.1070.21843
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110116
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_it0.7041.57965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.299212866
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79835044
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9024.54802
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: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 207 -
Rwork0.3 3908 -
obs--96.23 %

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