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- PDB-3ul2: Galactose-specific lectin from Dolichos lablab in P6522 space group -

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Basic information

Entry
Database: PDB / ID: 3ul2
TitleGalactose-specific lectin from Dolichos lablab in P6522 space group
ComponentsLegume lectin
KeywordsSUGAR BINDING PROTEIN / Legume lectin fold / Carbohydrate/Sugar-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 / Jelly Rolls ...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
beta-D-galactopyranose / : / DI(HYDROXYETHYL)ETHER / Lectin alpha chain
Similarity search - Component
Biological speciesDolichos lablab (antaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 10, 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)123,62226
Polymers121,8124
Non-polymers1,80922
Water3,009167
1
B: Legume lectin
D: Legume lectin
hetero molecules

B: Legume lectin
D: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,16120
Polymers121,8124
Non-polymers1,34916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
2
A: Legume lectin
C: Legume lectin
hetero molecules

A: Legume lectin
C: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,08232
Polymers121,8124
Non-polymers2,27028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Unit cell
Length a, b, c (Å)90.496, 90.496, 514.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 235
2113B1 - 235
3113C1 - 235
4113D1 - 235

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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
#4: 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 , 5 types, 185 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.5 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 4K, 100mM Tris, 200mM Lithium sulphate , pH 7.5, 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: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44836 / % possible obs: 93.4 % / Redundancy: 9.7 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 27.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2032 / % possible all: 95.7

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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: 2.5→50 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.158 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29624 2147 5 %RANDOM
Rwork0.27344 ---
obs0.27459 40489 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.259 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0.79 Å20 Å2
2---1.59 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7560 0 102 167 7829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227814
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.94410615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3125.11319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.192151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0761520
X-RAY DIFFRACTIONr_chiral_restr0.0690.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215808
X-RAY DIFFRACTIONr_mcbond_it0.5011.54916
X-RAY DIFFRACTIONr_mcangle_it0.9627923
X-RAY DIFFRACTIONr_scbond_it1.14232898
X-RAY DIFFRACTIONr_scangle_it2.1224.52692
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A940tight positional0.010.05
B940tight positional0.020.05
C940tight positional0.010.05
D940tight positional0.020.05
A849loose positional0.025
B849loose positional0.025
C849loose positional0.025
D849loose positional0.025
A940tight thermal0.030.5
B940tight thermal0.030.5
C940tight thermal0.030.5
D940tight thermal0.030.5
A849loose thermal0.0310
B849loose thermal0.0310
C849loose thermal0.0310
D849loose thermal0.0310
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 146 -
Rwork0.313 2794 -
obs--91.9 %

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