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- PDB-3uk9: Galactose-specific lectin from Dolichos lablab -

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Basic information

Entry
Database: PDB / ID: 3uk9
TitleGalactose-specific lectin from Dolichos lablab
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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lectin alpha chain
Similarity search - Component
Biological speciesDolichos lablab (antaque)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.11 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 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Legume lectin
F: Legume lectin
G: Legume lectin
H: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,96143
Polymers243,6258
Non-polymers2,33635
Water39622
1
A: Legume lectin
B: Legume lectin
C: Legume lectin
D: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,24624
Polymers121,8124
Non-polymers1,43320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Legume lectin
F: Legume lectin
G: Legume lectin
H: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,71519
Polymers121,8124
Non-polymers90315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.990, 84.130, 93.159
Angle α, β, γ (deg.)89.92, 76.01, 77.00
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Legume lectin /


Mass: 30453.115 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Dolichos lablab (antaque) / Tissue: Seed / References: UniProt: B3EWQ9*PLUS

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Non-polymers , 6 types, 57 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 6K, 100mM MES, 5% MPD , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 19, 2005 / Details: Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.11→90.17 Å / Num. obs: 41323 / % possible obs: 94.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.3
Reflection shellResolution: 3.11→3.19 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4092 / % possible all: 93.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJQ

1bjq


Resolution: 3.11→90.17 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.774 / SU B: 75.685 / SU ML: 0.61 / Cross valid method: THROUGHOUT / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30649 1820 5 %RANDOM
Rwork0.25087 ---
obs0.2537 34647 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.26 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å2-1.09 Å2-2.03 Å2
2---1.18 Å20.74 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.11→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14975 0 119 22 15116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215395
X-RAY DIFFRACTIONr_angle_refined_deg0.961.93420943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39951968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76525.08626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.709152311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1141539
X-RAY DIFFRACTIONr_chiral_restr0.0620.22429
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111566
X-RAY DIFFRACTIONr_mcbond_it0.1611.59832
X-RAY DIFFRACTIONr_mcangle_it0.299215818
X-RAY DIFFRACTIONr_scbond_it0.31435563
X-RAY DIFFRACTIONr_scangle_it0.5594.55125
LS refinement shellResolution: 3.11→3.191 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 123 -
Rwork0.357 2392 -
obs--89.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16450.82550.27742.88490.44073.54030.14760.116-0.0689-0.2479-0.0913-0.38250.43970.2419-0.05620.22240.17710.09280.19720.01010.245624.485-5.29926.116
21.75680.03250.31643.02861.27963.18990.1709-0.09260.2629-0.0667-0.1154-0.6487-0.28740.4584-0.05560.0874-0.12150.09850.31330.04430.47535.3525.53342.171
31.78550.1116-0.1584.2015-0.62272.98290.076-0.2635-0.2868-0.1356-0.0080.21050.3071-0.1352-0.06810.1873-0.0929-0.0480.29690.01060.24841.222-8.54447.859
42.7470.06250.23514.41380.11331.78090.2076-0.29940.18880.5228-0.1462-0.077-0.0717-0.1039-0.06150.2296-0.13830.02710.3907-0.13320.127610.1424.87561.647
51.11280.28760.35464.493-1.19824.35340.1541-0.13780.0076-0.01710.09260.31130.228-0.5832-0.24670.06610.01310.07230.3685-0.00760.3308-17.028-38.59218.899
61.81010.8207-1.15616.0585-2.64674.55270.07940.20120.5731-0.11030.14910.9153-1.0172-0.4782-0.22840.520.20160.00530.10120.08710.4169-13.186-5.6611.88
71.97240.9470.14254.17170.23993.84060.19430.1923-0.2435-0.02360.0109-0.08420.4250.1191-0.20520.19830.1563-0.08170.209-0.03950.20292.664-51.895-2.926
81.58160.1927-0.27194.3829-0.13272.631-0.19680.31320.181-0.46520.2045-0.0035-0.61710.3894-0.00770.5108-0.0915-0.00160.34690.11420.04949.446-18.701-16.695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 276
2X-RAY DIFFRACTION2B24 - 275
3X-RAY DIFFRACTION3C24 - 276
4X-RAY DIFFRACTION4D24 - 275
5X-RAY DIFFRACTION5E24 - 275
6X-RAY DIFFRACTION6F24 - 276
7X-RAY DIFFRACTION7G24 - 275
8X-RAY DIFFRACTION8H24 - 276

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