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- PDB-3zle: Crystal structure of Toxoplasma gondii sporozoite AMA1 -

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Basic information

Entry
Database: PDB / ID: 3zle
TitleCrystal structure of Toxoplasma gondii sporozoite AMA1
ComponentsAPICAL MEMBRANE ANTIGEN 1
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-like protein
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTonkin, M.L. / Boulanger, M.J.
CitationJournal: Plos One / Year: 2013
Title: Toxoplasma Gondii Sporozoites Invade Host Cells Using Two Novel Paralogs of Ron2 and Ama1
Authors: Poukchanski, A. / Tonkin, M.L. / Fritz, H.M. / Treeck, M. / Boulanger, M.J. / Boothroyd, J.C.
History
DepositionJan 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 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 1
B: APICAL MEMBRANE ANTIGEN 1
C: APICAL MEMBRANE ANTIGEN 1
D: APICAL MEMBRANE ANTIGEN 1
E: APICAL MEMBRANE ANTIGEN 1
F: APICAL MEMBRANE ANTIGEN 1
G: APICAL MEMBRANE ANTIGEN 1
H: APICAL MEMBRANE ANTIGEN 1
I: APICAL MEMBRANE ANTIGEN 1
J: APICAL MEMBRANE ANTIGEN 1
K: APICAL MEMBRANE ANTIGEN 1
L: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,48239
Polymers513,83312
Non-polymers3,64927
Water30,5351695
1
A: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3175
Polymers42,8191
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2254
Polymers42,8191
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2254
Polymers42,8191
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0043
Polymers42,8191
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2254
Polymers42,8191
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1333
Polymers42,8191
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1333
Polymers42,8191
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1333
Polymers42,8191
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9122
Polymers42,8191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9122
Polymers42,8191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0412
Polymers42,8191
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2254
Polymers42,8191
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.190, 155.520, 180.590
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
APICAL MEMBRANE ANTIGEN 1


Mass: 42819.445 Da / Num. of mol.: 12 / Fragment: CONSERVED ECTOPLASMIC REGION, RESIDUES 97-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Plasmid: PACGP67B / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B6K9M7
#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.: 9
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.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1695 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCORRECT SEQUENCE ONLY FOUND IN TOXODB TGME49_315730. RESIDUES 96-388 ARE IN THE UNP SEQUENCE, 389- ...CORRECT SEQUENCE ONLY FOUND IN TOXODB TGME49_315730. RESIDUES 96-388 ARE IN THE UNP SEQUENCE, 389-480 FOUND IN TOXODB

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.9 % / Description: NONE
Crystal growDetails: 1.0 M SUCCINIC ACID PH 7.0, 100 MM HEPES PH 7.0, 1% PEG MONOMETHYL ETHER 2000 AND 100 MM GLYCINE

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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→79.3 Å / Num. obs: 391285 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 75.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2Z

2x2z


Resolution: 2.35→78.04 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.353 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24393 20508 5 %RANDOM
Rwork0.20869 ---
obs0.21044 387902 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.013 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.01 Å2
2--0.16 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.35→78.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34720 0 234 1695 36649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0236023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.94249149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30354541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51725.331621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.655155262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1421599
X-RAY DIFFRACTIONr_chiral_restr0.1110.25237
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02128177
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 1491 -
Rwork0.331 27072 -
obs--94.45 %

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