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- PDB-3ujo: Galactose-specific seed lectin from Dolichos lablab in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3ujo
TitleGalactose-specific seed lectin from Dolichos lablab in complex with adenine and galactose
ComponentsLegume lectin
KeywordsSUGAR BINDING PROTEIN / Legume lectin fold / Carbohydrate-binding / Galactose / Adenine
Function / homology
Function and homology information


defense response to fungus / carbohydrate binding / killing of cells of another organism / defense response to bacterium
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, beta chain, Mn/Ca-binding site / Legume lectin domain / : / 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, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENINE / beta-D-galactopyranose / : / DI(HYDROXYETHYL)ETHER / Lectin alpha chain
Similarity search - Component
Biological speciesDolichos lablab (antaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShetty, K.N. / Latha, V.L. / Rao, R.N. / Nadimpalli, S.K. / Suguna, K.
CitationJournal: Iubmb Life / Year: 2013
Title: Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography.
Authors: Shetty, K.N. / Latha, V.L. / Rao, R.N. / Nadimpalli, S.K. / Suguna, K.
History
DepositionNov 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_asym_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_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legume lectin
B: Legume lectin
C: Legume lectin
D: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,97627
Polymers121,8124
Non-polymers2,16423
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.780, 89.780, 123.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Legume lectin


Mass: 30453.115 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dolichos lablab (antaque) / Tissue: Seed / References: UniProt: B3EWQ9*PLUS
#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 177 molecules

#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4K, 100mM Tris pH 8.5, 200mM Na-acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.253
11-H, H+K, -L20.248
11-h,-k,l30.248
11K, H, -L40.251
ReflectionResolution: 2→123.92 Å / Num. obs: 75331 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10855 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJQ

1bjq


Resolution: 2→42.2 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.402 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3754 5 %RANDOM
Rwork0.2075 ---
obs0.20966 71512 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.315 Å2
Baniso -1Baniso -2Baniso -3
1--10.32 Å20 Å20 Å2
2---10.32 Å20 Å2
3---20.64 Å2
Refinement stepCycle: LAST / Resolution: 2→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7661 0 130 158 7949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227950
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.94810812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26451000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06125.273330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1381520
X-RAY DIFFRACTIONr_chiral_restr0.0590.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215956
X-RAY DIFFRACTIONr_mcbond_it0.2011.54988
X-RAY DIFFRACTIONr_mcangle_it0.35828036
X-RAY DIFFRACTIONr_scbond_it0.36432962
X-RAY DIFFRACTIONr_scangle_it0.5474.52776
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 302 -
Rwork0.191 5039 -
obs--96.03 %

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