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- PDB-2auy: Pterocarpus angolensis lectin in complex with the trisaccharide G... -

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Basic information

Entry
Database: PDB / ID: 2auy
TitlePterocarpus angolensis lectin in complex with the trisaccharide GlcNAc(b1-2)Man(a1-3)Man
Componentslectin
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate / sugar / legume lectin
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 speciesPterocarpus angolensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsButs, L. / Garcia-Pino, A. / Imberty, A. / Amiot, N. / Boons, G.-J. / Beeckmans, S. / Versees, W. / Wyns, L. / Loris, R.
CitationJournal: Febs J. / Year: 2006
Title: Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin.
Authors: Buts, L. / Garcia-Pino, A. / Imberty, A. / Amiot, N. / Boons, G.-J. / Beeckmans, S. / Versees, W. / Wyns, L. / Loris, R.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _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 / pdbx_struct_conn_angle / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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 23, 2023Group: 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

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Assembly

Deposited unit
A: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4268
Polymers55,1172
Non-polymers1,3096
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.800, 83.140, 123.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsChains A and B in the asymmetric unit form together the physiological dimer

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Components

#1: Protein lectin


Mass: 27558.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / Tissue: seed / References: UniProt: Q8GSD2
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 559.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na-cacodylate, Na-acetate, PEG-8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2003
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 43030 / Num. obs: 43030 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→2 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.25 / Num. unique all: 3989 / % possible all: 92.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Q8P

1q8p


Resolution: 1.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.193 3494 random
Rwork0.175 --
all0.177 43030 -
obs0.177 43030 -
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 80 202 3991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00579
X-RAY DIFFRACTIONc_angle_deg1.533

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