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- PDB-5j51: Structure of tetrameric jacalin complexed with Gal alpha-(1,4) Gal -

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Basic information

Entry
Database: PDB / ID: 5j51
TitleStructure of tetrameric jacalin complexed with Gal alpha-(1,4) Gal
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 / 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 / DI(HYDROXYETHYL)ETHER / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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: 2016
Title: Effect of linkage on the location of reducing and nonreducing sugars bound to jacalin.
Authors: Abhinav, K.V. / Sharma, K. / Surolia, A. / Vijayan, M.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)69,36045
Polymers66,4718
Non-polymers2,88937
Water8,395466
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)34,44923
Polymers33,2354
Non-polymers1,21319
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-4 kcal/mol
Surface area15200 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)34,91122
Polymers33,2354
Non-polymers1,67618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint5 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.560, 81.090, 63.250
Angle α, β, γ (deg.)90.00, 108.05, 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, 10 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 alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(4+1)][a-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 501 molecules

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


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#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.: 466 / 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: 42.54 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 150mM 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 16, 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: 1.67→60.14 Å / Num. obs: 63612 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.16 Å2 / Rsym value: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2 / % possible all: 93.7

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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: 1.67→35.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.42 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21312 3223 5.1 %RANDOM
Rwork0.16445 ---
obs0.1669 60361 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.904 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.03 Å2
2--1.1 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.67→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 189 466 5220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024945
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9766669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7625607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95724.063192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51515729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.087159
X-RAY DIFFRACTIONr_chiral_restr0.1530.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213693
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: 1.665→1.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 236 -
Rwork0.397 4158 -
obs--92.47 %
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)
10.6486-0.1239-0.06180.8390.31641.0422-0.0025-0.0322-0.00320.04060.00460.00740.0047-0.0055-0.0020.01010.0023-0.00140.0026-0.00070.00114.38117.902336.3844
21.7562-0.4385-1.80220.50571.29774.72270.14820.15640.1179-0.1108-0.118-0.1001-0.3502-0.2908-0.03020.05470.02760.01180.05040.02410.08020.240911.876222.5152
30.9950.1589-0.10610.5523-0.1730.68340.0437-0.03110.05170.0229-0.020.0343-0.0607-0.0309-0.02370.01150.00050.00720.0221-0.00970.0094-20.79047.017422.8627
41.2037-1.5286-2.35325.14974.86945.9994-0.1107-0.1358-0.13620.08950.0472-0.01410.24980.14960.06350.02650.0118-0.00810.05070.02340.0617-8.8555-3.742522.8821
51.1326-0.13560.05030.755-0.15910.6990.02060.0737-0.0143-0.0524-0.0158-0.00030.01140.0435-0.00490.00750.00260.00490.0073-0.00020.006820.7526-2.65894.2628
60.84960.109-0.18620.35131.05683.6167-0.19920.0187-0.22470.1368-0.0520.01760.5229-0.19720.25110.139-0.01980.05580.0186-0.02220.09239.9347-9.947411.7112
70.63370.04460.00770.6871-0.04121.0230.00210.0749-0.0616-0.0604-0.02010.01470.0640.05040.0180.0152-0.00210.00040.021-0.00840.0071-4.3354-12.5892-4.4516
82.7409-1.6343-2.07372.05842.80823.88690.1550.04010.2227-0.19690.0471-0.1492-0.26930.0265-0.2020.035-0.00810.02030.05190.01420.0247-0.46850.92760.996
90.33010.0690.05120.0210.01080.00860.0120.03150.0585-0.0183-0.015-0.0029-0.00140.0120.0030.1767-0.0099-0.0060.16770.03240.16051.18993.556214.4384
101.08950.4159-0.54590.1666-0.25061.58660.05990.0960.01850.04060.02550.0437-0.07560.21-0.08550.23490.0053-0.01060.0595-0.01430.23084.37482.80425.383
110.2047-0.0044-0.00080.16430.06770.2574-0.00460.0069-0.0013-0.00080.0004-0.00560.00980.00750.00430.1199-0.0021-0.00530.09460.01790.12110.9965-0.259814.9523
12305.1877525.3754-75.4938910.5262-150.822190.465-0.40950.3008-2.73090.03780.8081-4.504-2.4533-1.167-0.39860.17560.04790.04030.02840.07240.37354.983625.239.3996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B4 - 18
3X-RAY DIFFRACTION3C1 - 133
4X-RAY DIFFRACTION4D3 - 17
5X-RAY DIFFRACTION5E1 - 133
6X-RAY DIFFRACTION6F4 - 18
7X-RAY DIFFRACTION7G1 - 133
8X-RAY DIFFRACTION8H4 - 18
9X-RAY DIFFRACTION9A201 - 203
10X-RAY DIFFRACTION9C201 - 210
11X-RAY DIFFRACTION9E201 - 211
12X-RAY DIFFRACTION9G201 - 204
13X-RAY DIFFRACTION10A204 - 206
14X-RAY DIFFRACTION10B101
15X-RAY DIFFRACTION10C211
16X-RAY DIFFRACTION10E212
17X-RAY DIFFRACTION11A301 - 419
18X-RAY DIFFRACTION11B201 - 211
19X-RAY DIFFRACTION11C301 - 392
20X-RAY DIFFRACTION11D101 - 112
21X-RAY DIFFRACTION11E301 - 400
22X-RAY DIFFRACTION11F101 - 109
23X-RAY DIFFRACTION11G301 - 405
24X-RAY DIFFRACTION11H101 - 118
25X-RAY DIFFRACTION12A207

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