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- PDB-3f53: Crystal structure of Toxoplasma gondii micronemal protein 1 bound... -

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Basic information

Entry
Database: PDB / ID: 3f53
TitleCrystal structure of Toxoplasma gondii micronemal protein 1 bound to 2F-3'SiaLacNAc
ComponentsMicronemal protein 1
KeywordsCELL ADHESION / micronemal protein / carbohydrate / fluorine / toxoplasma gondii / Cytoplasmic vesicle / Lectin / Virulence
Function / homology
Function and homology information


symbiont-mediated perturbation of host receptor-mediated signal transduction / effector-mediated perturbation of host innate immune response by symbiont / effector-mediated suppression of host innate immune response / microneme / Toll-like receptor 4 binding / Toll-like receptor 2 binding / sialic acid binding / host cell surface binding / immune system process / carbohydrate binding ...symbiont-mediated perturbation of host receptor-mediated signal transduction / effector-mediated perturbation of host innate immune response by symbiont / effector-mediated suppression of host innate immune response / microneme / Toll-like receptor 4 binding / Toll-like receptor 2 binding / sialic acid binding / host cell surface binding / immune system process / carbohydrate binding / cytoplasmic vesicle / host cell endosome / cell adhesion
Similarity search - Function
Actin; Chain A, domain 4 - #70 / Micronemal protein 1 / Micronemal protein 1, galectin-like domain / MIC1, C-terminal superfamily / Toxoplasma gondii micronemal protein 1 TgMIC1 / Micronemal adhesive repeat, sialic-acid binding / Sialic-acid binding micronemal adhesive repeat / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Micronemal protein 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarnett, J.A.
Citation
Journal: Protein Sci. / Year: 2009
Title: Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii.
Authors: Garnett, J.A. / Liu, Y. / Leon, E. / Allman, S.A. / Friedrich, N. / Saouros, S. / Curry, S. / Soldati-Favre, D. / Davis, B.G. / Feizi, T. / Matthews, S.
#1: Journal: Embo J. / Year: 2007
Title: Atomic resolution insight into host cell recognition by Toxoplasma gondii.
Authors: Blumenschein, T.M. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati- ...Authors: Blumenschein, T.M. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Micronemal protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,70816
Polymers27,2661
Non-polymers1,44215
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.361, 66.361, 172.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1066-

HOH

21A-1075-

HOH

31A-1159-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Micronemal protein 1


Mass: 27266.010 Da / Num. of mol.: 1 / Fragment: N-terminal domain: Residues 17-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: MIC1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): origami / References: UniProt: O00834
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose


Type: oligosaccharide / Mass: 473.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*F][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp2fluoro]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 188 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE NAG RESIDUE IS DISORDERED IN 2F-3'SIALACNAC AND NOT VISIBLE IN THE ELECTRON DENSITY, THEREFORE ...THE NAG RESIDUE IS DISORDERED IN 2F-3'SIALACNAC AND NOT VISIBLE IN THE ELECTRON DENSITY, THEREFORE IS MISSING IN THE FINAL STRUCTURE.

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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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 3.6M Ammonium acetate, 100mM Bis/tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→29.68 Å / Num. obs: 26571 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.021 Å2 / Rsym value: 0.075 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.246 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSC Quantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JH1

2jh1


Resolution: 2→29.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.816 / SU ML: 0.07 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19114 2663 10 %RANDOM
Rwork0.16783 ---
obs0.17024 23882 98.61 %-
all-26571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 95 174 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211890
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9822559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2525236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20823.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.4821516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21271
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.51209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27821869
X-RAY DIFFRACTIONr_scbond_it2.3773761
X-RAY DIFFRACTIONr_scangle_it3.524.5687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 188 -
Rwork0.197 1719 -
obs--98.91 %

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