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- PDB-2x2z: Crystal structure AMA1 from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 2x2z
TitleCrystal structure AMA1 from Toxoplasma gondii
ComponentsAPICAL MEMBRANE ANTIGEN 1, PUTATIVE
KeywordsMEMBRANE PROTEIN / INVASION / MOVING JUNCTION
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
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCrawford, J. / Tonkin, M.L. / Grujic, O. / Boulanger, M.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Characterization of Apical Membrane Antigen 1 (Ama1) from Toxoplasma Gondii.
Authors: Crawford, J. / Tonkin, M.L. / Grujic, O. / Boulanger, M.J.
History
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Atomic model / Non-polymer description ...Atomic model / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Apr 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 1.3Jul 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 1.4Oct 16, 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 / _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 1, PUTATIVE
B: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
D: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
E: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,9239
Polymers201,9464
Non-polymers9775
Water21,0781170
1
A: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7082
Polymers50,4861
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7082
Polymers50,4861
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8003
Polymers50,4861
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: APICAL MEMBRANE ANTIGEN 1, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7082
Polymers50,4861
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.150, 76.070, 88.250
Angle α, β, γ (deg.)72.19, 71.44, 72.90
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 50486.438 Da / Num. of mol.: 4 / Fragment: RESIDUES 64-519
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: B6KAM0
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1170 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→52.24 Å / Num. obs: 98629 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellHighest resolution: 2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 95.3

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.824 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4915 5 %RANDOM
Rwork0.18 ---
obs0.183 93713 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12427 0 62 1170 13659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02212870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.95117470
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85351554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0824.566622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.239152070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8371562
X-RAY DIFFRACTIONr_chiral_restr0.1550.21817
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219988
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_it1.1851.57837
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.024212661
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.27335033
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9724.54807
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→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 362 -
Rwork0.227 6801 -
obs--95.24 %

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