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- PDB-2xgg: Structure of Toxoplasma gondii Micronemal Protein 2 A_I Domain -

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Basic information

Entry
Database: PDB / ID: 2xgg
TitleStructure of Toxoplasma gondii Micronemal Protein 2 A_I Domain
ComponentsMICRONEME PROTEIN 2
KeywordsHYDROLASE / MICRONEME / MIC2 / A/I DOMAIN / CELL ADHESION
Function / homologyvon Willebrand factor, type A domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.05 Å
AuthorsTonkin, M.L. / Grujic, O. / Pearce, M. / Crawford, J. / Boulanger, M.J.
CitationJournal: Protein Sci. / Year: 2010
Title: Structure of the Micronemal Protein 2 (Mic2) A/I Domain from Toxoplasma Gondii.
Authors: Tonkin, M.L. / Grujic, O. / Pearce, M. / Crawford, J. / Boulanger, M.J.
History
DepositionJun 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MICRONEME PROTEIN 2
B: MICRONEME PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7103
Polymers38,6182
Non-polymers921
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-17.7 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.034, 63.034, 157.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MICRONEME PROTEIN 2


Mass: 19309.014 Da / Num. of mol.: 2 / Fragment: VWA INTEGRIN-LIKE DOMAIN, RESIDUES 26-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B6KIP6, arylesterase, EC: 3.4.24.14
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 47.6 % / Description: NONE
Crystal growDetails: 27% PEG3350, 0.1M HEPES 7.5, 0.2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→24.84 Å / Num. obs: 20754 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.69 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 10.82 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.05→24.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.173 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED BASED ON OVERLAYS WITH THE ALTERNATE CHAIN AND STEREOCHEMISTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27827 1065 5.1 %RANDOM
Rwork0.20644 ---
obs0.20991 19688 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 6 103 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.9653111
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25424.79296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31415399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1121512
X-RAY DIFFRACTIONr_chiral_restr0.1540.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211696
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_it1.3381.51459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26322360
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9813838
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4594.5751
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 78 -
Rwork0.252 1428 -
obs--100 %

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