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- PDB-3f5a: Crystal structure of Toxoplasma gondii micronemal protein 1 bound... -

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Basic information

Entry
Database: PDB / ID: 3f5a
TitleCrystal structure of Toxoplasma gondii micronemal protein 1 bound to 3'SiaLacNAc1-3
ComponentsMicronemal protein 1
KeywordsCELL ADHESION / cellular adhesion / micronemal protein / toxoplasma gondii / carbohydrate / fluorine / Cytoplasmic vesicle / Lectin / Virulence
Function / homology
Function and homology information


microneme / cytoplasmic vesicle / carbohydrate binding / 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. / Liu, Y. / Feizi, T. / Matthews, S.J.
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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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

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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)28,90916
Polymers27,2661
Non-polymers1,64315
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.226, 66.226, 172.188
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-1075-

HOH

21A-1159-

HOH

31A-1189-

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)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 203 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
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→33.17 Å / Num. obs: 23609 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.545 Å2 / Rsym value: 0.074 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 3837 / Rsym value: 0.2228 / % possible all: 100

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Processing

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

2jh1


Resolution: 2→27.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.514 / SU ML: 0.067 / 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
Rfree0.18875 2626 10 %RANDOM
Rwork0.16501 ---
obs0.16737 23609 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 109 189 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211891
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9932559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66523.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5571516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021444
X-RAY DIFFRACTIONr_nbd_refined0.20.2840
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.222
X-RAY DIFFRACTIONr_mcbond_it0.8711.51194
X-RAY DIFFRACTIONr_mcangle_it1.2321844
X-RAY DIFFRACTIONr_scbond_it2.3243779
X-RAY DIFFRACTIONr_scangle_it3.5484.5712
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 180 -
Rwork0.189 1754 -
obs-3398 99.95 %

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