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- PDB-1toq: CRYSTAL STRUCTURE OF A GALACTOSE SPECIFIC LECTIN FROM ARTOCARPUS ... -

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Basic information

Entry
Database: PDB / ID: 1toq
TitleCRYSTAL STRUCTURE OF A GALACTOSE SPECIFIC LECTIN FROM ARTOCARPUS HIRSUTA IN COMPLEX WITH METHYL-a-D-GALACTOSE
Components
  • AGGLUTININ ALPHA CHAIN
  • AGGLUTININ BETA CHAIN
KeywordsSUGAR BINDING PROTEIN / Artocarpus hirsuta / Moraceae plant lectins / Jacalin family / Post-translational modification / Carbohydrate specificity / Methyl--D-galactose / Three-dimensional structure / -prism I fold.
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-galactopyranoside / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus hirsutus (aini)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRao, K.N. / Suresh, C.G. / Katre, U.V. / Gaikwad, S.M. / Khan, M.I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl-alpha-D-galactose.
Authors: Rao, K.N. / Suresh, C.G. / Katre, U.V. / Gaikwad, S.M. / Khan, M.I.
History
DepositionJun 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 525SOLVENT MOLECULES SOLVENT MOLECULES 1 - 31 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 101- ...SOLVENT MOLECULES SOLVENT MOLECULES 1 - 31 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 101-130 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 201-227 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 301-329 ARE ASSOCIATED WITH COMPLEX A-B.
Remark 999SEQUENCE sEQUENCE OF THESE MOLECULES IS NOT YET AVAILABLE IN ANY SEQUENCE DATABASE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,44312
Polymers66,6668
Non-polymers7774
Water1,982110
1
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area8330 Å2
MethodPISA
2
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-6 kcal/mol
Surface area8220 Å2
MethodPISA
3
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9 kcal/mol
Surface area7820 Å2
MethodPISA
4
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-10 kcal/mol
Surface area7850 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-69 kcal/mol
Surface area24340 Å2
MethodPISA
6
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-22 kcal/mol
Surface area14410 Å2
MethodPISA
7
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28 kcal/mol
Surface area13500 Å2
MethodPISA
8
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-25 kcal/mol
Surface area14520 Å2
MethodPISA
9
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-25 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.372, 98.655, 164.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AGGLUTININ ALPHA CHAIN


Mass: 14605.298 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: SEEDS / Source: (natural) Artocarpus hirsutus (aini) / References: UniProt: P18670*PLUS
#2: Protein/peptide
AGGLUTININ BETA CHAIN


Mass: 2061.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P18673*PLUS
#3: Sugar
ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside / Methyl-α-D-galactose


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 6.5 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M PO4 BUFFER, 35% AMMONIUM SULPHATE,METHYL ALPHA GALACTOSE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 12, 2002 / Details: CONFOCAL
RadiationMonochromator: MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. all: 50815 / Num. obs: 50815 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 42.52 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.53
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.13 / Num. unique all: 5103 / % possible all: 98.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 2.5→15 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R FACTOR / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 2358 RANDOM
Rwork0.197 --
all-50815 -
obs-46666 -
Displacement parametersBiso mean: 47.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 52 110 4726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg2.2
LS refinement shellResolution: 2.5→2.6 Å
RfactorNum. reflection% reflection
Rfree0.29 293 -
Rwork0.24 --
obs-5783 93.1 %

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