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- PDB-5j50: Structure of tetrameric jacalin complexed with Gal beta-(1,3) Gal... -

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Basic information

Entry
Database: PDB / ID: 5j50
TitleStructure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / Plant lectins / 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
Thomsen-Friedenreich antigen / P-NITROPHENOL / DI(HYDROXYETHYL)ETHER / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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: To Be Published
Title: Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP
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 / 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 / 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.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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)69,41129
Polymers66,4718
Non-polymers2,94121
Water7,692427
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)34,71515
Polymers33,2354
Non-polymers1,47911
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-9 kcal/mol
Surface area14560 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)34,69714
Polymers33,2354
Non-polymers1,46110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-10 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.530, 81.650, 66.890
Angle α, β, γ (deg.)90.00, 100.00, 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, 12 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)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen / 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
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 444 molecules

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


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.38 Å3/Da / Density % sol: 48 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 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 12, 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: 2.04→51.27 Å / Num. obs: 39076 / Biso Wilson estimate: 12.5 Å2
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.3 / % possible all: 91.3

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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: 2.05→51.27 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.405 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.189 / Details: HYDROGENS HAVE NOT BEEN USED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3892 10 %RANDOM
Rwork0.182 ---
obs0.187 35165 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.03 Å2
2--0.41 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→51.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4521 0 195 427 5143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024835
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9876560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5075586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76424.011187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.206158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213648
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: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 284 -
Rwork0.274 2425 -
obs--96.06 %
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)
11.77980.2882-0.2571.0076-0.18991.40150.0636-0.05150.09480.0103-0.0160.0845-0.0971-0.0665-0.04760.01270.0049-0.00160.0065-0.00450.0195-20.163816.476523.0628
24.734-3.1783-1.59863.79183.75254.9292-0.2709-0.027-0.14340.42970.13520.11460.51160.23860.13570.07540.01970.02350.03850.04250.0659-8.37035.476923.6183
30.8992-0.2177-0.15921.11710.45921.25890.0043-0.15640.00870.12340.0187-0.02970.02060.0505-0.0230.0158-0.0045-0.00150.0296-0.00370.00575.035318.687135.9173
43.8674-0.4868-2.31140.10360.69595.45960.20860.28930.1877-0.0865-0.039-0.0354-0.6233-0.2089-0.16960.13230.01160.03060.02320.01440.06841.368221.330621.0337
51.8241-0.0004-0.38761.0354-0.00271.68970.0190.2085-0.076-0.1119-0.0285-0.00320.0790.03240.00950.01990.0099-0.00710.0284-0.01030.0152-3.8079-3.4369-3.7655
61.61290.31530.37870.8965-0.02940.10820.07090.01390.1867-0.266-0.1258-0.10230.02430.01470.05490.21470.05960.07490.05890.01590.0506-0.121210.15161.334
71.5064-0.3068-0.11621.3018-0.00660.81240.03970.1603-0.0038-0.0701-0.0369-0.0811-0.03020.0666-0.00280.0093-0.0054-0.00440.03690.01390.02321.20956.31764.9759
84.9003-1.1735-5.38141.30222.403612.5774-0.11970.0761-0.00240.20010.04-0.03640.3852-0.14150.07970.0439-0.0035-0.01830.01560.0070.0210.4193-0.195512.6061
90.35290.0087-0.05730.18070.09440.2230.00570.004-0.03280.0114-0.00260.01950.00740.0367-0.0030.16480.0084-0.00060.10580.02020.12431.76179.087315.6394
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 - 18
5X-RAY DIFFRACTION5E1 - 133
6X-RAY DIFFRACTION6F4 - 18
7X-RAY DIFFRACTION7G1 - 133
8X-RAY DIFFRACTION8H4 - 18
9X-RAY DIFFRACTION9A301 - 387
10X-RAY DIFFRACTION9B101 - 110
11X-RAY DIFFRACTION9C401 - 507
12X-RAY DIFFRACTION9D101 - 110
13X-RAY DIFFRACTION9E301 - 403
14X-RAY DIFFRACTION9F201 - 208
15X-RAY DIFFRACTION9G301 - 394
16X-RAY DIFFRACTION9H201 - 208

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