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- PDB-4z81: Crystal structure of AMA4 DI-DII-EGF1 from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 4z81
TitleCrystal structure of AMA4 DI-DII-EGF1 from Toxoplasma gondii
ComponentsEGF family domain-containing protein
KeywordsMEMBRANE PROTEIN / Apicomplexa / invasion / moving junction / parasite / PAN domain
Function / homology
Function and homology information


EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
EGF family domain-containing protein / EGF family domain-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsParker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP82915 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Dissecting the interface between apicomplexan parasite and host cell: Insights from a divergent AMA-RON2 pair.
Authors: Parker, M.L. / Penarete-Vargas, D.M. / Hamilton, P.T. / Guerin, A. / Dubey, J.P. / Perlman, S.J. / Spano, F. / Lebrun, M. / Boulanger, M.J.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGF family domain-containing protein
B: EGF family domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5034
Polymers111,3192
Non-polymers1842
Water12,196677
1
A: EGF family domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7512
Polymers55,6591
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EGF family domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7512
Polymers55,6591
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.220, 202.590, 72.800
Angle α, β, γ (deg.)90.000, 100.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EGF family domain-containing protein


Mass: 55659.262 Da / Num. of mol.: 2 / Fragment: residues 58-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_294330 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: V4YLU4, UniProt: S7UIL3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Bis-Tris pH 6.0, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2013
RadiationMonochromator: ACCEL/BRUKER double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→50.65 Å / Num. all: 66314 / Num. obs: 66314 / % possible obs: 95.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.1 / % possible all: 91.3

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4Z80

4z80


Resolution: 2.05→49.094 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 3357 5.07 %random selection
Rwork0.1721 62901 --
obs0.174 66258 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.11 Å2 / Biso mean: 35.5797 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 2.05→49.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 12 677 8306
Biso mean--33.06 37.77 -
Num. residues----996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037870
X-RAY DIFFRACTIONf_angle_d0.78210650
X-RAY DIFFRACTIONf_chiral_restr0.031146
X-RAY DIFFRACTIONf_plane_restr0.0031385
X-RAY DIFFRACTIONf_dihedral_angle_d11.852826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07930.22951330.24172374250787
2.0793-2.11030.29721370.24812509264692
2.1103-2.14330.31221360.24132563269993
2.1433-2.17840.27071410.22952577271893
2.1784-2.2160.29911550.232508266393
2.216-2.25630.27061330.22342543267693
2.2563-2.29970.27451240.21532606273093
2.2997-2.34660.23121340.19822517265192
2.3466-2.39770.2281300.19712532266293
2.3977-2.45340.23651410.19092619276093
2.4534-2.51480.21021260.19612520264693
2.5148-2.58280.22531610.18762554271594
2.5828-2.65880.25831520.18532603275595
2.6588-2.74460.24431310.19492596272795
2.7446-2.84270.2541420.19492675281796
2.8427-2.95650.24631530.17972633278697
2.9565-3.0910.21511500.18482696284698
3.091-3.25390.19671320.17652769290198
3.2539-3.45780.1971410.17022717285899
3.4578-3.72470.19561470.153927272874100
3.7247-4.09930.17371570.140527412898100
4.0993-4.69210.151440.122827802924100
4.6921-5.90990.16411330.138627522885100
5.9099-49.1080.18721240.16152790291499

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