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- PDB-1eis: UDA UNCOMPLEXED FORM. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTIN... -

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Basic information

Entry
Database: PDB / ID: 1eis
TitleUDA UNCOMPLEXED FORM. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II
ComponentsPROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V)
KeywordsSUGAR BINDING PROTEIN / LECTIN / HEVEIN DOMAIN / UDA / SUPERANTIGEN
Function / homologyChitin-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 / chitin binding / Agglutinin isolectin VI
Function and homology information
Biological speciesUrtica dioica (great nettle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.66 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
DepositionFeb 28, 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: 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 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V)


Theoretical massNumber of molelcules
Total (without water)9,3501
Polymers9,3501
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.300, 41.600, 77.100
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 PROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V) / 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: UniProt: Q9SYR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe structure comprises two hevein-like domains, each homologous to those of Wheat Germ Agglutinin ...The structure comprises two hevein-like domains, each homologous to those of Wheat Germ Agglutinin (PDB code: 9wga). Each domain contains a saccharide-binding site. The N-terminal residue is pyrrolidone carboxylic acid (PCA). A dual conformation is seen at Gly79, Gly80. No electron density is seen for the side chain of Arg33 beyond the CB atom. No interpretable density is seen for C-terminal residues Ser87, Ser88, and Ser89.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
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
16-12 mg/mlprotein1drop
250 mMsodium acetate1reservoir
30.1 Msodium chloride1reservoir
46 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 1.66→18 Å / Num. all: 11689 / Num. obs: 11689 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.7
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.352 / Num. unique all: 1015 / % possible all: 84.7
Reflection shell
*PLUS
% possible obs: 84.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMmodel building
REFMACrefinement
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.66→18 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was determined to 2.45A resolution by MIR methods based on 4 Hg derivatives (rotating-anode X-ray source) with solvent flattening, and refined to 1.66A resolution with ...Details: The structure was determined to 2.45A resolution by MIR methods based on 4 Hg derivatives (rotating-anode X-ray source) with solvent flattening, and refined to 1.66A resolution with synchrotron data using a bulk solvent correction and anisotropic scale factor.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 602 -RANDOM
Rwork0.191 ---
all0.207 11689 --
obs0.207 11689 95.4 %-
Refinement stepCycle: LAST / Resolution: 1.66→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 0 49 680
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0160.02
X-RAY DIFFRACTIONp_planar_d0.0220.03
X-RAY DIFFRACTIONp_plane_restr0.01160.02
X-RAY DIFFRACTIONp_chiral_restr0.1850.15
X-RAY DIFFRACTIONp_singtor_nbd0.1490.3
X-RAY DIFFRACTIONp_multtor_nbd0.1620.3
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_transverse_tor27.420
X-RAY DIFFRACTIONp_mcbond_it1.8142
X-RAY DIFFRACTIONp_mcangle_it2.8643
X-RAY DIFFRACTIONp_scbond_it3.3973
X-RAY DIFFRACTIONp_scangle_it4.9164

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