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- PDB-2ll4: HADDOCK structure of TgMIC4-A5/lacto-N-biose complex, based on NO... -

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Basic information

Entry
Database: PDB / ID: 2ll4
TitleHADDOCK structure of TgMIC4-A5/lacto-N-biose complex, based on NOE-derived distance restraints
ComponentsMicronemal protein 4
KeywordsCELL ADHESION
Function / homology
Function and homology information


microneme / cytoplasmic vesicle / cell adhesion / proteolysis / extracellular region
Similarity search - Function
PAN domain / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Micronemal protein 4
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsCowper, B. / Matthews, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Galactose Recognition by the Apicomplexan Parasite Toxoplasma gondii.
Authors: Marchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Liew, L. / Chai, W. / Childs, R.A. / Saouros, S. / Simpson, P. / Roque Barreira, M. ...Authors: Marchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Liew, L. / Chai, W. / Childs, R.A. / Saouros, S. / Simpson, P. / Roque Barreira, M.C. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
History
DepositionOct 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
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_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Micronemal protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5422
Polymers9,1581
Non-polymers3831
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Micronemal protein 4


Mass: 9158.231 Da / Num. of mol.: 1 / Fragment: Apple-5 domain residues 410-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: MIC4, TgIb.0680 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B (DE3) / References: UniProt: Q9XZH7
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC aromatic
2222D 1H-1H TOCSY
2322D DQF-COSY
2422D 1H-1H NOESY
2522D 1H-13C HSQC
1613D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 uM [U-98% 13C; U-98% 15N] TgMIC4-A5, 20 mM potassium phosphate, 100 mM sodium chloride, 500 uM Lacto-N-biose, 90% H2O/10% D2O90% H2O/10% D2O
210 mM Lacto-N-biose, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMTgMIC4-A5-1[U-98% 13C; U-98% 15N]1
20 mMpotassium phosphate-21
100 mMsodium chloride-31
500 uMLacto-N-biose-41
10 mMLacto-N-biose-52
Sample conditionsIonic strength: 0.7 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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