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- PDB-4okr: Structures of Toxoplasma gondii MIC2 -

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Basic information

Entry
Database: PDB / ID: 4okr
TitleStructures of Toxoplasma gondii MIC2
ComponentsMicronemal protein MIC2
KeywordsCELL ADHESION / VWA domain / integrin I domain / TSR domain / Adhesin / gliding motility / cell surface
Function / homology
Function and homology information


Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Micronemal protein MIC2
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsSong, G. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of the Toxoplasma gliding motility adhesin.
Authors: Song, G. / Springer, T.A.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Micronemal protein MIC2
B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4374
Polymers60,0762
Non-polymers3602
Water1,04558
1
A: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2182
Polymers30,0381
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2182
Polymers30,0381
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.791, 148.052, 41.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Micronemal protein MIC2 / Microneme protein MIC2


Mass: 30038.109 Da / Num. of mol.: 2 / Fragment: MIC2 (unp residues 67-337) / Mutation: S158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_201780 / Cell line (production host): HEK293T / Production host: homo sapiens (human) / References: UniProt: O00816
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M (NH4)2SO4, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.3 Å / Num. all: 15742 / Num. obs: 15634 / % possible obs: 99.3 % / Observed criterion σ(F): 100 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.268
Reflection shellResolution: 2.6→2.64 Å / % possible all: 63.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1565)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→43.3 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 783 5.01 %
Rwork0.23 --
obs0.2323 15634 92.23 %
all-15742 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 22 58 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033674
X-RAY DIFFRACTIONf_angle_d0.7344994
X-RAY DIFFRACTIONf_dihedral_angle_d14.6271367
X-RAY DIFFRACTIONf_chiral_restr0.029578
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.76410.3819950.3171813X-RAY DIFFRACTION70
2.7641-2.97750.3291200.28852264X-RAY DIFFRACTION86
2.9775-3.2770.33381350.26482567X-RAY DIFFRACTION97
3.277-3.7510.30831410.22172682X-RAY DIFFRACTION100
3.751-4.72490.21691410.19272683X-RAY DIFFRACTION100
4.7249-43.40150.261510.2252842X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.7955 Å / Origin y: 34.9748 Å / Origin z: 9.8997 Å
111213212223313233
T0.2473 Å2-0.004 Å2-0.0663 Å2-0.3085 Å2-0.0232 Å2--0.2918 Å2
L0.7551 °21.0883 °2-0.773 °2-1.6577 °2-0.9272 °2--1.2401 °2
S-0.0439 Å °0.1213 Å °0.0574 Å °-0.0722 Å °0.0821 Å °0.0831 Å °0.0383 Å °-0.1049 Å °-0.0401 Å °
Refinement TLS groupSelection details: all

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