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- PDB-1ws4: Crystal structure of Jacalin- Me-alpha-Mannose complex: Promiscui... -

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Basic information

Entry
Database: PDB / ID: 1ws4
TitleCrystal structure of Jacalin- Me-alpha-Mannose complex: Promiscuity vs Specificity
Components
  • (Agglutinin alpha ...) x 2
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / Beta-prism-I fold / Post translational proteolysis / lectin / galactose-specific
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-galactopyranoside / methyl alpha-D-glucopyranoside / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsJeyaprakash, A.A. / Jayashree, G. / Mahanta, S.K. / Sekar, K. / Surolia, A. / Vijayan, M.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity
Authors: Jeyaprakash, A.A. / Jayashree, G. / Mahanta, S.K. / Swaminathan, C.P. / Sekar, K. / 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.
History
DepositionOct 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 25, 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: 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)67,53512
Polymers66,7598
Non-polymers7774
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-77 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.287, 99.416, 105.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Agglutinin alpha ... , 2 types, 4 molecules AGCE

#1: Protein Agglutinin alpha chain / Jacalin alpha chain


Mass: 14643.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: UniProt: P18670
#3: Protein Agglutinin alpha chain / Jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: UniProt: P18670

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Protein/peptide / Non-polymers , 2 types, 258 molecules BDFH

#2: Protein/peptide
Agglutinin beta-3 chain / Jacalin beta-3 chain


Mass: 2031.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: UniProt: P18673
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Sugar ChemComp-GYP / methyl alpha-D-glucopyranoside / METHYL-ALPHA-D-GLUCOPYRANOSIDE / ALPHA-METHYL-D-GLUCOPYRANOSIDE / methyl alpha-D-glucoside / methyl D-glucoside / methyl glucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGlcp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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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: 3.1 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 25% PEG 4K, 0.2M ammonium sulphate, 0.1M sodium acetate trihydrate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 2004 / Details: osmic mirrors
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 66297 / Num. obs: 65845 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.381 / Num. unique all: 6474 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1UGW

1ugw


Resolution: 1.9→28.06 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2056586.88 / 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
Rfree0.205 3314 5 %RANDOM
Rwork0.184 ---
obs0.184 65793 99.1 %-
all-66297 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5795 Å2 / ksol: 0.323272 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2---0.74 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 54 254 4916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.02
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 562 5.3 %
Rwork0.234 10132 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CIS.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
X-RAY DIFFRACTION5GYP.PARAM

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