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- PDB-1kuj: Crystal structure of Jacalin complexed with 1-O-methyl-alpha-D-mannose -

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Basic information

Entry
Database: PDB / ID: 1kuj
TitleCrystal structure of Jacalin complexed with 1-O-methyl-alpha-D-mannose
Components
  • JACALIN ALPHA CHAIN
  • JACALIN BETA CHAIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / BETA-PRISM FOLD / CARBOHYDRATE BINDING
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Agglutinin alpha chain / Agglutinin beta-1 chain
Similarity search - Component
Biological speciesArtocarpus integer (chempedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBourne, Y. / Astoul, C.H. / Zamboni, V. / Peumans, W.J. / Menu-Bouaouiche, L. / Van Damme, E.J.M. / Barre, A. / Rouge, P.
CitationJournal: 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
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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.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 1.4Aug 16, 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: JACALIN ALPHA CHAIN
B: JACALIN BETA CHAIN
C: JACALIN ALPHA CHAIN
D: JACALIN BETA CHAIN
E: JACALIN ALPHA CHAIN
F: JACALIN BETA CHAIN
G: JACALIN ALPHA CHAIN
H: JACALIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,95912
Polymers66,1828
Non-polymers7774
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-73 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.795, 82.612, 63.482
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTETRAMER OF FOUR ALPHA CHAINS ASSOCIATED WITH FOUR BETA CHAINS. THIS ENTRY CONTAINS A COMPLETE TETRAMER

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Components

#1: Protein
JACALIN ALPHA CHAIN / Agglutinin alpha chain


Mass: 14673.479 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / References: UniProt: P18670
#2: Protein/peptide
JACALIN BETA CHAIN / Agglutinin beta chain


Mass: 1872.064 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / References: UniProt: P18671
#3: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8K, 10% ISOPROPANOL (V/V), 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.4
2150 mM1dropNaCl
318.5 mg/mlprotein1drop
420-22 %PEG80001reservoir
510 %(v/v)isopropanol1reservoir
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 2, 2000
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2→33 Å / Num. obs: 38447 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 9.1 Å2 / Rsym value: 0.038 / Net I/σ(I): 9.5
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 38468 / Num. measured all: 140888 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 88.5 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1KU8

1ku8


Resolution: 2→19.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1509605.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 797 2.1 %RANDOM
Rwork0.191 ---
obs0.191 38431 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8744 Å2 / ksol: 0.330889 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å212.4 Å2
2---6.42 Å20 Å2
3---6.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 52 305 4954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 138 2.3 %
Rwork0.275 5988 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MMA.PARMMA.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.75
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / Rfactor Rwork: 0.275

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