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- PDB-1k7t: Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,6Gal c... -

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Basic information

Entry
Database: PDB / ID: 1k7t
TitleCrystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,6Gal complex
Componentsagglutinin isolectin 3
KeywordsSUGAR BINDING PROTEIN / Hevein-type fold
Function / homology
Function and homology information


chitin binding / catalytic activity / carbohydrate binding
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Agglutinin isolectin 3
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMuraki, M. / Ishimura, M. / Harata, K.
Citation
Journal: Biochim.Biophys.Acta / Year: 2002
Title: Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence
Authors: Muraki, M. / Ishimura, M. / Harata, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: X-ray structure of wheat germ agglutinin isolectin 3
Authors: Harata, K. / Nagahora, H. / Jigami, Y.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose
Authors: Harata, K. / Muraki, M.
#3: Journal: Protein Eng. / Year: 2000
Title: Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin
Authors: Muraki, M. / Morii, H. / Harata, K.
History
DepositionOct 22, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Refinement description
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / software / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 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 / 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 / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: agglutinin isolectin 3
B: agglutinin isolectin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2734
Polymers37,5062
Non-polymers7672
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-21 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.15, 93.17, 45.10
Angle α, β, γ (deg.)90.00, 110.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein agglutinin isolectin 3 / WGA3


Mass: 18752.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P10969
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: sodium acetate, Calcium Chloride, Ethanol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Details: Harata, K., (1995) Acta Crystallogr., Sect.D, 51, 1013.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mgWGA311
210 mMacetate12pH4.9
36 mM12CaCl2
44 %(v/v)ethanol12

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Dec 29, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29 Å / Num. obs: 32097 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.4→2.45 Å / Rmerge(I) obs: 0.249
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 13176 / Num. measured all: 32097

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Processing

Software
NameVersionClassification
MADNESSdata collection
X-PLORmodel building
X-PLOR3.1refinement
MADNESSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native WGA3

Resolution: 2.4→8 Å / σ(F): 2 / Details: Avarage B-value are for protein atoms
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1107 10 %random
Rwork0.242 ---
obs-11077 --
Displacement parametersBiso mean: 28.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 52 69 2467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.96
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_improper_angle_d1.65
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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