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- PDB-1en2: UDA TETRASACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA A... -

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Basic information

Entry
Database: PDB / ID: 1en2
TitleUDA TETRASACCHARIDE 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 / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / 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
: / Lectin/endochitinase 1
Similarity search - Component
Biological speciesUrtica dioica (great nettle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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. / Damme, E.J. / 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 20, 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 1.3Feb 5, 2014Group: Other
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 / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _atom_site.occupancy / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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)10,1812
Polymers9,3501
Non-polymers8311
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.820, 39.600, 63.640
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 THE 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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 N-TERMINAL RESIDUE IS PYRROLIDONE CARBOXYLIC ACID (PCA). A DUAL CONFORMATION IS SEEN for all or part of the residue at LEU15, GLU28, SER45, ASN74. NO INTERPRETABLE DENSITY IS SEEN FOR C-TERMINAL RESIDUES SER87, SER88, AND SER89. 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 tetrasaccharide 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: 2.13 Å3/Da / Density % sol: 42.25 %
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
23 mMtetrasaccharide1drop
350 mMsodium acetate1reservoir
40.1 Msodium chloride1reservoir
56 %PEG60001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONLURE D41A11.375
SYNCHROTRONLURE DW3220.966
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJul 6, 1999
MARRESEARCH2IMAGE PLATEJul 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.3751
20.9661
ReflectionResolution: 1.4→25 Å / Num. all: 15524 / Num. obs: 15524 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.328 / Num. unique all: 1473 / % possible all: 94.2
Reflection
*PLUS
Num. obs: 15499
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIS

1eis


Resolution: 1.4→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
Rfree0.203 766 -RANDOM
Rwork0.189 ---
all0.198 15499 --
obs0.198 15499 96.2 %-
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms660 0 56 76 792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0150.02
X-RAY DIFFRACTIONp_planar_d0.0170.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.1320.15
X-RAY DIFFRACTIONp_singtor_nbd0.1520.3
X-RAY DIFFRACTIONp_multtor_nbd0.210.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.820
X-RAY DIFFRACTIONp_mcbond_it1.4662
X-RAY DIFFRACTIONp_mcangle_it2.2913
X-RAY DIFFRACTIONp_scbond_it2.3873
X-RAY DIFFRACTIONp_scangle_it3.5554
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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