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- PDB-5jm1: Structure of tetrameric jacalin complexed with a trisaccharide, G... -

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Basic information

Entry
Database: PDB / ID: 5jm1
TitleStructure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal beta-(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
methyl alpha-D-galactopyranoside / DI(HYDROXYETHYL)ETHER / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 28, 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.mon_nstd_flag / _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)67,89621
Polymers66,4718
Non-polymers1,42513
Water7,260403
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)33,65210
Polymers33,2354
Non-polymers4166
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-26 kcal/mol
Surface area13750 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)34,24411
Polymers33,2354
Non-polymers1,0097
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-13 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 81.580, 63.000
Angle α, β, γ (deg.)90.00, 107.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 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

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Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][a2112h-1a_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside / Methyl-α-D-galactose


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 414 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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.: 403 / 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: 42.92 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.4
Details: 100 mM HEPES (pH 7.4), 15% poly(ethylene glycol) 8000, 10% (v/v) isopropanol

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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 28, 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: 1.95→46.01 Å / Num. obs: 38922 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.132 / Net I/σ(I): 8.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.7 / % possible all: 91

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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: 1.95→46.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.031 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 3871 9.9 %RANDOM
Rwork0.18036 ---
obs0.18618 35043 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.1 Å2
2--0.36 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.95→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 94 403 5043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9686443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30324.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55415694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.073158
X-RAY DIFFRACTIONr_chiral_restr0.1150.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213588
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 267 -
Rwork0.261 2413 -
obs--89.87 %
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)
11.0756-0.0162-0.10420.8460.3211.1130.0018-0.04820.02680.05760.0151-0.0111-0.0219-0.0062-0.01690.0340.0008-0.00760.0203-0.00210.02014.58488.100436.2393
23.1178-2.0467-3.24841.36731.81038.10730.193-0.18480.3715-0.11470.1463-0.2553-0.33180.0096-0.33930.0961-0.05040.02680.0689-0.04520.0910.364212.444122.6206
31.31540.2524-0.35430.6588-0.50350.97620.0641-0.01770.04230.0109-0.03710.0875-0.076-0.0615-0.0270.04650.0074-0.00320.0358-0.01480.0449-20.64437.021922.7183
40.77850.4097-0.04563.46653.6484.7421-0.19550.0196-0.08080.26860.05610.08770.5035-0.02520.13940.1203-0.00230.01320.02490.00370.0418-8.1595-3.842322.1818
51.1238-0.1531-0.10710.6917-0.04610.86860.05370.0356-0.0244-0.0785-0.0269-0.0286-0.02920.0677-0.02680.0342-0.00160.00060.02360.00310.040620.7598-2.60074.2755
62.6965-1.0127-2.67721.2542.46737.0648-0.17210.0162-0.11160.16590.0309-0.02260.4098-0.08190.14110.0569-0.0077-0.00980.0141-0.00880.051110.102-9.847411.6924
71.10320.0669-0.19460.78790.05081.2222-0.01910.076-0.0494-0.0479-0.0113-0.00640.05360.01950.03040.0416-0.00710.00090.0212-0.00480.0244-4.2732-12.4745-4.4946
82.45260.8788-0.13922.06861.65231.66250.21860.16310.0373-0.2082-0.1136-0.1003-0.3003-0.1816-0.1050.12350.0384-0.00670.05340.03030.0373-0.03070.8335-0.0904
90.19320.0011-0.03150.16650.04690.2868-0.00220.00640.01120.0005-0.0032-0.0237-0.0124-0.00210.00540.1181-0.0023-0.01320.07940.02190.11760.75481.169614.6904
100.5632-0.1797-0.71050.08260.20860.9376-0.03530.0679-0.08870.03630.0010.09240.1144-0.09070.03430.2779-0.0414-0.02160.1359-0.01970.258-5.5405-0.867617.7946
111.381216.3765-29.8874194.2411-354.49646.94453.8629-0.31230.3935-3.19340.45464.64285.83746.7374-4.31750.50440.049-0.00030.1433-0.25320.8312-32.265310.694914.9215
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 - 16
5X-RAY DIFFRACTION5E1 - 133
6X-RAY DIFFRACTION6F4 - 18
7X-RAY DIFFRACTION7G1 - 133
8X-RAY DIFFRACTION8H4 - 18
9X-RAY DIFFRACTION9A301 - 405
10X-RAY DIFFRACTION9B101 - 110
11X-RAY DIFFRACTION9C301 - 382
12X-RAY DIFFRACTION9D201 - 205
13X-RAY DIFFRACTION9E301 - 391
14X-RAY DIFFRACTION9F101 - 107
15X-RAY DIFFRACTION9G301 - 387
16X-RAY DIFFRACTION9H101 - 116
17X-RAY DIFFRACTION10A201 - 203
18X-RAY DIFFRACTION10C201
19X-RAY DIFFRACTION10D101
20X-RAY DIFFRACTION10E201
21X-RAY DIFFRACTION10G201 - 204
22X-RAY DIFFRACTION11C202

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