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- PDB-1jac: A NOVEL MODE OF CARBOHYDRATE RECOGNITION IN JACALIN, A MORACEAE P... -

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Basic information

Entry
Database: PDB / ID: 1jac
TitleA NOVEL MODE OF CARBOHYDRATE RECOGNITION IN JACALIN, A MORACEAE PLANT LECTIN WITH A BETA-PRISM
Components(JACALIN) x 2
KeywordsLECTIN / NON-LEGUME / BETA-PRISM FOLD / CARBOHYDRATE SPECIFICITY / GLYCOPROTEIN
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-1 chain
Similarity search - Component
Biological speciesArtocarpus heterophyllus (jackfruit)
MethodX-RAY DIFFRACTION / Resolution: 2.43 Å
AuthorsSankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold.
Authors: Sankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M.
#1: Journal: Biochem.J. / Year: 1992
Title: Primary Structure of a Thomsen-Friedenreich-Antigen-Specific Lectin, Jacalin [Artocarpus Integrifolia (Jack Fruit) Agglutinin]. Evidence for the Presence of an Internal Repeat
Authors: Mahanta, S.K. / Sanker, S. / Rao, N.V. / Swamy, M.J. / Surolia, A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Preparation and X-Ray Characterization of Four New Crystal Forms of Jacalin, a Lectin from Artocarpus Integrifolia
Authors: Banerjee, R. / Dhanaraj, V. / Mahanta, S.K. / Surolia, A. / Vijayan, M.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Preparation and Preliminary X-Ray Studies of Two Crystal Forms of the Anti-T Lectin from Jackfruit (Artocarpus Integrifolia)
Authors: Dhanaraj, V. / Patanjali, S.R. / Surolia, A. / Vijayan, M.
History
DepositionMay 22, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: JACALIN
B: JACALIN
C: JACALIN
D: JACALIN
E: JACALIN
F: JACALIN
G: JACALIN
H: JACALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,72812
Polymers66,9518
Non-polymers7774
Water5,819323
1
A: JACALIN
B: JACALIN
C: JACALIN
D: JACALIN
hetero molecules

A: JACALIN
B: JACALIN
C: JACALIN
D: JACALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,72812
Polymers66,9518
Non-polymers7774
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area12120 Å2
ΔGint-74 kcal/mol
Surface area24950 Å2
MethodPISA, PQS
2
E: JACALIN
F: JACALIN
G: JACALIN
H: JACALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8646
Polymers33,4754
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-75 kcal/mol
Surface area24010 Å2
MethodPISA
3
E: JACALIN
F: JACALIN
G: JACALIN
H: JACALIN
hetero molecules

E: JACALIN
F: JACALIN
G: JACALIN
H: JACALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,72812
Polymers66,9518
Non-polymers7774
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
MethodPQS
Unit cell
Length a, b, c (Å)129.600, 129.600, 157.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6499, -0.5848, 0.4854), (-0.6032, 0.0084, -0.7976), (0.4623, -0.8111, -0.3582)82.5843, 168.729, 150.36279
2given(-0.9999, 0.0117, -0.0036), (-0.0117, -0.9999, -0.0081), (-0.0037, -0.0081, 1)94.2333, 130.7878, 0.5545
3given(0.6533, 0.5879, 0.4771), (0.5988, -0.0155, -0.8008), (-0.4634, 0.8088, -0.3622)-54.3179, 113.4668, 89.4544
4given(-0.6522, -0.6122, 0.447), (-0.5738, 0.0133, -0.8189), (0.4954, -0.7906, -0.3599)88.0688, 168.7312, 146.97749
5given(-0.9998, -0.0017, 0.02), (0.0117, -0.9999, 0.0022), (0.02, 0.0022, 0.9998)93.2502, 129.24699, -1.3612
6given(0.6613, 0.5888, 0.4648), (0.5913, -0.0279, -0.806), (-0.4616, 0.8078, -0.3666)-53.8325, 114.6377, 89.6184
DetailsTHERE ARE TWO HALF TETRAMERS IN THE ASYMMETRIC UNIT EACH WITH 222 SYMMETRY. THE HEAVY CHAIN IS NUMBERED FROM 1 TO 133 AND THE LIGHT CHAIN IS NUMBERED FROM 1 TO 20. THE HEAVY AND THE LIGHT CHAIN ARE PART OF THE SAME SUBUNIT AND ARE SEPARATED BY A POST-TRANSLATIONAL CLEAVAGE.

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Components

#1: Protein
JACALIN / / JACKFRUIT AGGLUTININ


Mass: 14673.479 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus heterophyllus (jackfruit) / References: UniProt: P18670
#2: Protein/peptide
JACALIN / / JACKFRUIT AGGLUTININ


Mass: 2064.257 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus heterophyllus (jackfruit) / References: UniProt: P18671
#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.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 58 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
20.02 Mphosphate1drop
30.1 M1dropNaCl
40.05 %(w/v)1dropNaN3
560 Mmethyl-alpha-D-galactopyranoside1drop
65-6 %(w/v)PEG40001drop
740 %PEG40001reservoir
80.02 Mphosphate1reservoir
90.1 M1reservoirNaCl
100.05 %(w/v)1reservoirNaN3
1160 Mmethyl-alpha-D-galactopyranoside1reservoir

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Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23791 / % possible obs: 78 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2.43 Å / Num. measured all: 219402

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
RefinementResolution: 2.43→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.174 --
obs0.174 20822 70.4 %
Refinement stepCycle: LAST / Resolution: 2.43→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 52 323 4955
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_deg1.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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