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- PDB-4oku: Structure of Toxoplasma gondii proMIC2 -

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Basic information

Entry
Database: PDB / ID: 4oku
TitleStructure of Toxoplasma gondii proMIC2
ComponentsMicronemal protein MIC2
KeywordsCELL ADHESION / VWA / integrin I domain / TSR domain / Adhesin / gliding motility
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: 3.2 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,0594
Polymers67,6982
Non-polymers3602
Water0
1
A: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers33,8491
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers33,8491
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Micronemal protein MIC2
hetero molecules

B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0594
Polymers67,6982
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area2300 Å2
ΔGint-5 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.434, 159.321, 41.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 33849.133 Da / Num. of mol.: 2 / Fragment: proMIC2 (unp residues 30-337) / Mutation: S158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_201780 / Production host: homo sapiens (human) / References: UniProt: O00816
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


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

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: 0.2 M (NH4)2SO4 and 20% PEG 3350, pH 3.7, VAPOR DIFFUSION, HANGING DROP, 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: Jun 29, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→45.4 Å / Num. all: 10125 / Num. obs: 8867 / % possible obs: 87.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.26 Å / % possible all: 65.8

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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: 3.2→45.39 Å / SU ML: 0.49 / σ(F): 0.09 / Phase error: 39.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3198 426 5 %random
Rwork0.2638 ---
obs0.2667 8513 84.48 %-
all-10125 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 22 0 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023732
X-RAY DIFFRACTIONf_angle_d0.6565072
X-RAY DIFFRACTIONf_dihedral_angle_d13.4721387
X-RAY DIFFRACTIONf_chiral_restr0.026588
X-RAY DIFFRACTIONf_plane_restr0.003654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.66310.45641100.36582102X-RAY DIFFRACTION68
3.6631-4.61440.31311510.26682858X-RAY DIFFRACTION90
4.6144-45.39470.29311650.23813127X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -13.1906 Å / Origin y: 38.8039 Å / Origin z: -10.8478 Å
111213212223313233
T0.4511 Å2-0.0177 Å20.0085 Å2-0.4013 Å2-0.0572 Å2--0.4254 Å2
L0.8886 °2-0.015 °20.0846 °2-0.4521 °2-0.3736 °2--0.566 °2
S-0.1038 Å °0.2913 Å °0.1163 Å °0.1372 Å °0.1003 Å °0.0554 Å °0.0413 Å °-0.1232 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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