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- PDB-1lu1: THE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1lu1
TitleTHE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE FORSSMAN DISACCHARIDE
ComponentsLECTIN
KeywordsLECTIN / LEGUME LECTINS / FORSSMAN DISACCHARIDE / DOLICHOS BIFLORUS SEED LECTIN
Function / homology
Function and homology information


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
Forssman antigen fragment / ADENINE / : / Seed lectin subunit I
Similarity search - Component
Biological speciesVigna unguiculata subsp. cylindrica (catjang cowpea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHamelryck, T.W. / Loris, R. / Bouckaert, J. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.
Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E.
History
DepositionJul 24, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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.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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7705
Polymers27,1151
Non-polymers6554
Water00
1
A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,07820
Polymers108,4604
Non-polymers2,61816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)79.050, 79.050, 260.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein LECTIN / DBL


Mass: 27115.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DOLICHOS BIFLORUS SEED LECTIN
Source: (gene. exp.) Vigna unguiculata subsp. cylindrica (catjang cowpea)
Species: Vigna unguiculata / Strain: subsp. cylindrica / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P05045
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / Forssman antigen fragment


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Forssman antigen fragment
DescriptorTypeProgram
DGalpNAca1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-FucpNAc]{[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: 100 MM HEPES PH 7.5 0.2 M MGCL2 30% (W/V) PEG 400
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mMadenine1drop
3100 mMHEPES1reservoir
40.2 M1reservoirMgCl2
530 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 13175 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.27 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 91892 / Rmerge(I) obs: 0.146
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAT

1fat


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1350 10.2 %RANDOM
Rwork0.194 ---
obs0.194 13174 100 %-
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 40 0 1921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
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: 2.6→2.69 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 134 10.5 %
Rwork0.355 1145 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.08
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor obs: 0.355

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