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- PDB-4r6o: Jacalin-carbohydrate interactions. Distortion of the ligand as a ... -

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Basic information

Entry
Database: PDB / ID: 4r6o
TitleJacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / Galactose specific lectin / beta-prism I fold / post translational proteolysis / T-antigen binding protein / Plant lectins / Galactose
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
alpha-D-galactopyranose / ISOPROPYL ALCOHOL / 4-METHYL-2H-CHROMEN-2-ONE / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAbhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity.
Authors: Abhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes.
Authors: Jeyaprakash, A.A. / Geetha Rani, P. / Banuprakash Reddy, G. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M.
#3: Journal: J.Mol.Biol. / Year: 2003
Title: Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study.
Authors: Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
#4: Journal: J.Mol.Biol. / Year: 2005
Title: Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity.
Authors: Arockia Jeyaprakash, A. / Jayashree, G. / Mahanta, S.K. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
#5: Journal: Biochem.J. / Year: 2002
Title: Structural basis for the unusual carbohydrate-binding specificity of jacalin towards galactose and mannose.
Authors: Bourne, Y. / Astoul, C.H. / Zamboni, V. / Peumans, W.J. / Menu-Bouaouiche, L. / Van Damme, E.J. / Barre, A. / Rouge, P.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Dec 4, 2019Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn
Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 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.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,61729
Polymers66,4718
Non-polymers2,14621
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-84 kcal/mol
Surface area23110 Å2
MethodPISA
2
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9769
Polymers33,2354
Non-polymers7415
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-31 kcal/mol
Surface area13140 Å2
MethodPISA
3
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,64120
Polymers33,2354
Non-polymers1,40616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-31 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.590, 82.180, 63.310
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 12 molecules ACEGBDFH

#1: Protein
Agglutinin alpha chain / Jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-20 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18670
#2: Protein/peptide
Agglutinin beta-3 chain / Jacalin beta-3 chain


Mass: 1944.170 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18673
#4: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


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

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Non-polymers , 4 types, 690 molecules

#3: Chemical
ChemComp-ZZ1 / 4-METHYL-2H-CHROMEN-2-ONE / 4-METHYLUMBELLIFERYL


Mass: 160.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% PEG 8000, 0.1M HEPES, pH 7.4, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2013 / Details: Bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→60.62 Å / Num. all: 83181 / Num. obs: 83181 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.089 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.55-1.634.11.9120780.5591100
1.63-4.94.28.2831810.089199.9
4.9-28.054.117.626650.065198.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KU8

1ku8


Resolution: 1.6→28.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.034 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21877 3805 5 %RANDOM
Rwork0.18092 ---
all0.18287 83181 --
obs0.18287 71859 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.066 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20.44 Å2
2--1.48 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 148 673 5382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024837
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9836565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7824.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.919158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213660
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 251 -
Rwork0.288 5212 -
obs--99.98 %

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