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- PDB-3zld: Crystal structure of Toxoplasma gondii sporozoite AMA1 in complex... -

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Basic information

Entry
Database: PDB / ID: 3zld
TitleCrystal structure of Toxoplasma gondii sporozoite AMA1 in complex with a 36 aa region of sporozoite RON2
Components
  • APICAL MEMBRANE ANTIGEN 1
  • RHOPTRY NECK PROTEIN 2
KeywordsMEMBRANE PROTEIN / MOVING JUNCTION / INVASION
Function / homology
Function and homology information


host cell plasma membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Complement Module; domain 1 - #70 / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Complement Module; domain 1 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Apical membrane antigen 1-like protein / Rhoptry neck protein 2-like protein 2
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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 1
B: RHOPTRY NECK PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)46,9272
Polymers46,9272
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-22.1 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.370, 124.180, 171.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21A-2005-

HOH

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Components

#1: Protein APICAL MEMBRANE ANTIGEN 1


Mass: 42819.445 Da / Num. of mol.: 1 / Fragment: CONSERVED ECTOPLASMIC REGION, RESIDUES 97-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B6K9M7
#2: Protein/peptide RHOPTRY NECK PROTEIN 2


Mass: 4107.623 Da / Num. of mol.: 1 / Fragment: D3 REGION, RESIDUES 452-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Plasmid: PET32A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: B6KLP1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCORRECT SEQUENCE ONLY FOUND IN TOXODB, GENE TGME49_315730

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M HEPES PH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / 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: 3.1→85.96 Å / Num. obs: 9716 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.5 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZLE CHAIN A

3zle


Resolution: 3.1→85.96 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.855 / SU B: 19.85 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26334 961 9.9 %RANDOM
Rwork0.20494 ---
obs0.2109 8701 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.451 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.22 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 3.1→85.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 0 7 2981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023057
X-RAY DIFFRACTIONr_bond_other_d0.0020.022761
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9424167
X-RAY DIFFRACTIONr_angle_other_deg0.7153.0066372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5765390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88425.522134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.93115460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.16158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
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_it2.8644.91569
X-RAY DIFFRACTIONr_mcbond_other2.8644.8991568
X-RAY DIFFRACTIONr_mcangle_it4.8027.3421956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1795.0791488
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: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 69 -
Rwork0.311 598 -
obs--91.5 %

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