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- PDB-5j4x: Structure of tetrameric jacalin complexed with Gal beta-(1,3) Gal... -

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Basic information

Entry
Database: PDB / ID: 5j4x
TitleStructure of tetrameric jacalin complexed with Gal beta-(1,3) Gal-beta-OMe
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / Plant lectins and sugar binding protein / Galactose specific lectin / beta-prism I fold / post translational proteolysis / T-antigen binding protein / reducing and non-reducing sugars
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
ISOPROPYL ALCOHOL / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAbhinav, K.V. / Sharma, K. / Surolia, A. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology, Govt. of India India
CitationJournal: IUBMB Life / Year: 2017
Title: Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with beta-substituted disaccharides.
Authors: Abhinav, K.V. / Sharma, K. / Surolia, A. / Vijayan, M.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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)67,81825
Polymers66,4718
Non-polymers1,34717
Water9,998555
1
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)34,14814
Polymers33,2354
Non-polymers91310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-17 kcal/mol
Surface area13950 Å2
MethodPISA
2
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)33,67011
Polymers33,2354
Non-polymers4347
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-16 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.629, 82.181, 63.060
Angle α, β, γ (deg.)90.00, 107.42, 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, 9 molecules ACEGBDFH

#1: Protein
Agglutinin alpha chain / Jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 4 / 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
#3: Polysaccharide beta-D-galactopyranose-(1-3)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 571 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.3 Å3/Da / Density % sol: 43.6 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM HEPES buffer (pH 7.4), 150 mM NaCl, 15% poly(ethylene glycol) 8000, 10% (v/v) isopropanol, 100mM HEPES (pH 7.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 25, 2015 / Details: 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: 1.65→35.71 Å / Num. obs: 66777 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 10.18 Å2 / Rsym value: 0.219 / Net I/σ(I): 10.5
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.9 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLM1.0.5data reduction
SCALAdata scaling
PHASER2.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KU8

1ku8


Resolution: 1.65→35.71 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.732 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.117 / Details: HYDROGENS HAVE NOT BEEN USED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24027 3396 5.1 %RANDOM
Rwork0.19387 ---
obs0.19629 63357 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.27 Å2
2--0.55 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.65→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 88 555 5217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024788
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9616477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52624.227194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.358158
X-RAY DIFFRACTIONr_chiral_restr0.1440.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.645→1.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 174 -
Rwork0.398 2896 -
obs--61.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4949-0.31550.2951.00390.37981.3998-0.0305-0.21350.15820.092-0.0163-0.0176-0.0653-0.02280.04680.0177-0.004-0.00430.0411-0.02890.0244.91798.692136.2387
24.3313-1.5635-4.46241.42853.51419.31270.06840.13830.3033-0.246-0.0481-0.0497-0.4502-0.19-0.02030.0801-0.00810.02190.0091-0.00540.07431.485911.936720.6493
31.34630.2181-0.37280.9837-0.28871.26010.044-0.010.0850.0119-0.01890.0541-0.122-0.1078-0.02510.01230.01090.00210.0123-0.00230.0073-20.2857.341222.905
42.8947-1.8513-2.1875.98294.92526.5673-0.2429-0.1745-0.25150.31880.10830.10030.53110.1340.13460.04840.01330.01780.02730.01720.0229-7.8458-3.635322.7488
51.5549-0.22210.01381.0273-0.15760.9650.04240.0628-0.0595-0.1494-0.006-0.1137-0.06960.1319-0.03640.0325-0.01410.01610.0246-0.00270.037521.2389-2.29054.5703
61.9907-0.5984-0.84162.83262.40666.5038-0.1501-0.1085-0.36470.2106-0.0125-0.03150.4288-0.10060.16260.0337-0.00040.02510.00940.01920.077810.1028-9.520612.727
71.0902-0.061-0.16720.98150.06511.2904-0.02140.0995-0.0993-0.0929-0.02690.03070.1144-0.01760.04830.020200.00250.0095-0.00960.0105-3.8031-12.2635-4.1601
81.1701-0.7976-1.78473.75063.9115.03430.23470.12730.246-0.23260.0406-0.0952-0.4381-0.1302-0.27530.0580.04110.03020.05170.00030.07920.00081.16121.0667
90.37480.13040.19090.04880.06490.12680.06040.0075-0.04530.0109-0.01640.0049-0.05550.0343-0.0440.31640.01630.00170.29050.00140.2597-3.10870.298913.6412
100.2737-0.0165-0.0250.18290.06780.29560.00230.00340.0202-0.0112-0.0089-0.0129-0.0106-0.00040.00650.1279-0.0005-0.01150.10550.00910.133-0.5830.178213.6267
11523.1677-197.9623-347.830774.9074131.6162231.257-3.1007-11.19731.21531.10814.075-0.45781.9527.4425-0.97430.1732-0.0443-0.10590.60480.11980.086411.06262.014719.6249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B3 - 18
3X-RAY DIFFRACTION3C1 - 133
4X-RAY DIFFRACTION4D3 - 17
5X-RAY DIFFRACTION5E1 - 133
6X-RAY DIFFRACTION6F3 - 18
7X-RAY DIFFRACTION7G1 - 133
8X-RAY DIFFRACTION8H4 - 18
9X-RAY DIFFRACTION9A201 - 203
10X-RAY DIFFRACTION9C201 - 204
11X-RAY DIFFRACTION9D101
12X-RAY DIFFRACTION9E201 - 202
13X-RAY DIFFRACTION9F101
14X-RAY DIFFRACTION9G201 - 203
15X-RAY DIFFRACTION9H101
16X-RAY DIFFRACTION10A301 - 418
17X-RAY DIFFRACTION10B101 - 118
18X-RAY DIFFRACTION10C301 - 434
19X-RAY DIFFRACTION10D201 - 210
20X-RAY DIFFRACTION10E301 - 415
21X-RAY DIFFRACTION10F201 - 210
22X-RAY DIFFRACTION10G301 - 437
23X-RAY DIFFRACTION10H201 - 213
24X-RAY DIFFRACTION11A204

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