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- PDB-1m26: Crystal structure of jacalin-T-antigen complex -

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Basic information

Entry
Database: PDB / ID: 1m26
TitleCrystal structure of jacalin-T-antigen complex
Components
  • Jacalin, alpha chain
  • Jacalin, beta chain
KeywordsSUGAR BINDING PROTEIN / PLANT PROTEIN / All beta sheet protein / beta prism I fold
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
Thomsen-Friedenreich antigen / : / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsJeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Surolia, A. / Vijayan, M.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexs
Authors: Jeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / 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.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: 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)66,86312
Polymers65,3298
Non-polymers1,5334
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-48 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.92, 78.00, 67.91
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsBiological molecule is a tetramer. There is one tetramer in the assymmetric unit

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Components

#1: Protein
Jacalin, alpha chain / AGGLUTININ ALPHA CHAIN


Mass: 14673.479 Da / Num. of mol.: 4 / Fragment: residues 85-217 of GB sequence entry AA32678 / Source method: isolated from a natural source
Details: synonymous scientific name: Artocarpus heterophyllus
Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: GenBank: 289162, UniProt: P18670*PLUS
#2: Protein/peptide
Jacalin, beta chain / AGGLUTININ BETA CHAIN


Mass: 1658.874 Da / Num. of mol.: 4 / Fragment: residues 64-78 of GB sequence entry AA32678 / Source method: isolated from a natural source
Details: synonymous scientific name: Artocarpus heterophyllus
Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: GenBank: 289162, UniProt: P18673*PLUS
#3: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, 0.02M phosphate buffer at pH 7.3, VAPOR DIFFUSION, HANGING DROP at 298K
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 %(w/v)PEG40001drop
640 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.62→19.58 Å / Num. all: 76669 / Num. obs: 74262 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 1.8 % / Num. unique all: 3714 / % possible all: 95.8
Reflection
*PLUS
% possible obs: 96.7 % / Num. measured all: 188335
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 3714 / Rmerge(I) obs: 0.289

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JAC

1jac


Resolution: 1.62→19.58 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3787 5.1 %RANDOM
Rwork0.189 ---
obs0.189 74262 96.7 %-
all-76669 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5119 Å2 / ksol: 0.345509 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å2-0.61 Å2
2--6.74 Å20 Å2
3----3.74 Å2
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.62→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 104 497 5185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.69
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.372.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 675 5.5 %
Rwork0.291 11692 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMTAN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.69

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