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- PDB-1ugx: Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-G... -

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Basic information

Entry
Database: PDB / ID: 1ugx
TitleCrystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / All beta sheet protein / Beta-prism I fold / 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
Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (chempedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
Citation
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.
#1: 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. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M.
#2: 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.
History
DepositionJun 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1003
Polymers16,7032
Non-polymers3971
Water2,216123
1
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40012
Polymers66,8118
Non-polymers1,5904
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area15180 Å2
ΔGint-56 kcal/mol
Surface area23030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.287, 100.556, 102.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-285-

HOH

21A-287-

HOH

31A-288-

HOH

41A-290-

HOH

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Components

#1: Protein Agglutinin alpha chain / Jacalin alpha chain


Mass: 14643.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / Organ: seeds / References: UniProt: P18670
#2: Protein/peptide Agglutinin beta-3 chain / Jacalin beta-3 chain


Mass: 2059.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / Organ: seeds / References: UniProt: P18673
#3: Polysaccharide beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAc[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_1*OC_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.08 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, NaCl, sodium azide, Phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.02 Mphosphate1droppH7.3
30.1 M1dropNaCl
40.025 %(w/v)sodium azide1drop
58-10 %PEG40001drop
640 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 27418 / Num. obs: 27418 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.163 / Num. unique all: 2452
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Num. measured all: 139555
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 83 % / Num. unique obs: 2452

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→26.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1230623.38 / 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 1344 4.9 %RANDOM
Rwork0.189 ---
obs0.189 27409 91.3 %-
all-27418 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0741 Å2 / ksol: 0.353446 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--2.11 Å20 Å2
3----3.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 27 123 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 183 4.5 %
Rwork0.326 3907 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CIS.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MTN.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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