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- PDB-1enm: UDA TRISACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGG... -

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Basic information

Entry
Database: PDB / ID: 1enm
TitleUDA TRISACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II
ComponentsAGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI
KeywordsSUGAR BINDING PROTEIN / LECTIN / HEVEIN DOMAIN / UDA / SUPERANTIGEN / SACCHARIDE BINDING
Function / homology
Function and homology information


chitinase activity / chitinase / chitin catabolic process / chitin binding / defense response to fungus / polysaccharide catabolic process / cell wall macromolecule catabolic process / carbohydrate binding / killing of cells of another organism / metal ion binding
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / 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 / Lysozyme-like domain superfamily
Similarity search - Domain/homology
triacetyl-beta-chitotriose / : / Lectin/endochitinase 1
Similarity search - Component
Biological speciesUrtica dioica (great nettle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaul, F.A. / Rovira, P. / Boulot, G. / Van Damme, E.J.M. / Peumans, W.J. / Truffa-Bachi, P. / Bentley, G.A.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
Authors: Saul, F.A. / Rovira, P. / Boulot, G. / Van Damme, E.J.M. / Peumans, W.J. / Truffa-Bachi, P. / Bentley, G.A.
#1: Journal: Plant Mol.Biol. / Year: 1999
Title: Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family
Authors: Does, M.P. / Ng, D.K. / Dekker, H.L. / Peumans, W.J. / Houterman, P.M. / Van Damme, E.J. / Cornelissen, B.J.C.
History
DepositionMar 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: 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: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _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 3.1Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9782
Polymers9,3501
Non-polymers6281
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.780, 46.160, 57.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI / UDA


Mass: 9350.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED FROM RHIZOMES / Source: (natural) Urtica dioica (great nettle) / References: GenBank: 4138900, UniProt: P11218*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe structure comprises two hevein-like domains, each containing a distinct saccharide-binding site. ...The structure comprises two hevein-like domains, each containing a distinct saccharide-binding site. The two binding sites are located at opposite extremities of the molecule. The principal binding-site residues are SER 19, TRP 21, TRP 23, and TYR 30 on the first domain, and the homologous residues SER 65, HIS 67, TRP 69, and TYR 76 on the second domain. The crystallographic asymmetric unit contains one molecule of UDA and a single trisaccharide ligand. The ligand interacts simultaneously with the binding site on the N-terminal domain of one molecule and that of the C-terminal domain of a symmetry-related molecule.

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6000, sodium acetate, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
Crystal grow
*PLUS
PH range low: 6.5 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
29 mMtrisaccharide1drop
350 mMsodium acetate1reservoir
40.1 Msodium chloride1reservoir
56 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 8284 / Num. obs: 8284 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.473 / Num. unique all: 817 / % possible all: 98
Reflection
*PLUS
Num. obs: 8283
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIS
Resolution: 1.9→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was determined by molecular replacement methods based on the uncomplexed UDA structure (1EIS). A bulk solvent correction was applied.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 423 -RANDOM
Rwork0.201 ---
all0.206 8283 --
obs0.206 8283 96.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms660 0 42 37 739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0150.02
X-RAY DIFFRACTIONp_planar_d0.0180.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.1580.15
X-RAY DIFFRACTIONp_singtor_nbd0.150.3
X-RAY DIFFRACTIONp_multtor_nbd0.1750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor4.87
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.320
X-RAY DIFFRACTIONp_mcbond_it1.7632
X-RAY DIFFRACTIONp_mcangle_it2.6673
X-RAY DIFFRACTIONp_scbond_it2.7363
X-RAY DIFFRACTIONp_scangle_it4.224
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS

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