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- PDB-1qoo: lectin UEA-II complexed with NAG -

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Basic information

Entry
Database: PDB / ID: 1qoo
Titlelectin UEA-II complexed with NAG
ComponentsCHITIN BINDING LECTIN, UEA-II
KeywordsLECTIN / CARBOHYDRATE BINDING / N-ACETYLGLUCOSAMINE
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesULEX EUROPAEUS (furze)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLoris, R. / De Greve, H. / Dao-Thi, M.-H. / Messens, J. / Imberty, A. / Wyns, L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural Basis of Carbohydrate Recognition by Lectin II from Ulex Europaeus, a Protein with a Promiscuous Carbohydrate Binding Site
Authors: Loris, R. / De Greve, H. / Dao-Thi, M.-H. / Messens, J. / Imberty, A. / Wyns, L.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1999
Title: Novel Structures of Plant Lectins and Their Complexes with Carbohydrates
Authors: Bouckaert, J. / Hamelryck, T.W. / Wyns, L. / Loris, R. / Hamelryck, T.W.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: The Quaternary Structure of Uea-II, the Chitobiose Specific Lectin from Gorse
Authors: Dao-Thi, M.-H. / Rizkallah, P. / Wyns, L. / Poortmans, F. / Loris, R.
#3: Journal: Biochim.Biophys.Acta / Year: 1998
Title: Legume Lectin Structure
Authors: Loris, R. / Hamelryck, T.W. / Bouckaert, J. / Wyns, L.
History
DepositionNov 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 1.5Dec 13, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 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: CHITIN BINDING LECTIN, UEA-II
B: CHITIN BINDING LECTIN, UEA-II
C: CHITIN BINDING LECTIN, UEA-II
D: CHITIN BINDING LECTIN, UEA-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,30119
Polymers104,3724
Non-polymers1,92915
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.480, 104.480, 175.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
CHITIN BINDING LECTIN, UEA-II


Mass: 26093.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ULEX EUROPAEUS (furze) / Organ: SEED / References: GenBank: AF190633, UniProt: Q9FVF8*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Dao-Thi M.H., (1998) Acta Crystallog. sect., D54, 844.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0-5.0 mg/mlprotein1drop
2100 mMcacodylate1reservoiror MES
38-16 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 29125 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.42 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 10.64
Reflection shellResolution: 2.75→2.84 Å / Redundancy: 4.96 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.6 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 162577
Reflection shell
*PLUS
% possible obs: 97.5 % / Num. unique obs: 2223 / Num. measured obs: 11024

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNLIGANDED UEA-II (1QNW)

1qnw


Resolution: 2.75→20 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2345 8.1 %RANDOM
Rwork0.174 ---
obs0.174 29125 99.2 %-
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 109 0 7277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.497
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.906
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.222
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.75→2.84 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3125 302 8.5 %
Rwork0.2483 3246 -
obs--97.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.906
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.222
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / Rfactor obs: 0.251

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