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- PDB-5y97: Crystal structure of snake gourd seed lectin in complex with lactose -

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Basic information

Entry
Database: PDB / ID: 5y97
TitleCrystal structure of snake gourd seed lectin in complex with lactose
Components(Seed lectin) x 3
KeywordsPLANT PROTEIN / beta-trefoil / Lectin
Function / homology
Function and homology information


rRNA N-glycosylase activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2640 / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2640 / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Helix non-globular / Special / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-lactose / Seed lectin
Similarity search - Component
Biological speciesTrichosanthes anguina (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsChandran, T. / Vijayan, M. / Sivaji, N. / Surolia, A.
Funding support India, 1items
OrganizationGrant numberCountry
India
Citation
Journal: Glycobiology / Year: 2018
Title: Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study
Authors: Chandran, T. / Sivaji, N. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.
Authors: Sharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M.
History
DepositionAug 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: 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: Seed lectin
B: Seed lectin
C: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2286
Polymers57,3223
Non-polymers9063
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, each lectin chain binds to a sugar molecule for type II RIPs. But SGSL binds only to single sugar molecule
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-45 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.429, 109.429, 232.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 2 molecules BC

#2: Protein Seed lectin / SGSL


Mass: 23387.219 Da / Num. of mol.: 1 / Fragment: UNP residues 47-255 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8
#3: Protein Seed lectin / SGSL


Mass: 29287.674 Da / Num. of mol.: 1 / Fragment: UNP residues 256-519 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8

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Protein/peptide / Non-polymers , 2 types, 6 molecules A

#1: Protein/peptide Seed lectin / SGSL


Mass: 4647.276 Da / Num. of mol.: 1 / Fragment: UNP residues 4-44 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#4: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Sequence detailsThere are three different polypeptide chains. A and B are contiguous and are results from cleavage. ...There are three different polypeptide chains. A and B are contiguous and are results from cleavage. C is an independent chain.

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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: 3.51 Å3/Da / Density % sol: 64.93 % / Description: hexagonal crystals
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: reservoir solution contained 4M sodium formate / PH range: 6.4-7.9

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2015
RadiationMonochromator: si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.05→94.77 Å / Num. obs: 16493 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.146 / Net I/σ(I): 13.3
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 19.5 % / Rmerge(I) obs: 1.534 / Mean I/σ(I) obs: 2 / Num. unique obs: 2340 / CC1/2: 0.808 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.2data reduction
SCALA3.3.22data scaling
PHASER2.7.15phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR6

4hr6


Resolution: 3.05→94.77 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 45.997 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25067 782 4.8 %RANDOM
Rwork0.22154 ---
obs0.22287 15645 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 118.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.84 Å2-0 Å2
2--1.69 Å2-0 Å2
3----5.47 Å2
Refinement stepCycle: 1 / Resolution: 3.05→94.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 60 5 4039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194118
X-RAY DIFFRACTIONr_bond_other_d0.0030.023681
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9615617
X-RAY DIFFRACTIONr_angle_other_deg1.16938546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79525190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96415658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9561520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
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_it4.695.8372041
X-RAY DIFFRACTIONr_mcbond_other4.695.8382040
X-RAY DIFFRACTIONr_mcangle_it7.0728.7662546
X-RAY DIFFRACTIONr_mcangle_other7.0718.7662547
X-RAY DIFFRACTIONr_scbond_it6.1386.5622077
X-RAY DIFFRACTIONr_scbond_other6.1376.5672078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1699.6833072
X-RAY DIFFRACTIONr_long_range_B_refined13.7217079
X-RAY DIFFRACTIONr_long_range_B_other13.72117079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 55 -
Rwork0.373 1122 -
obs--100 %
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)
16.5528-0.605-2.1560.50711.16079.40660.187-0.58891.4492-0.42970.5239-0.5632-1.51920.9459-0.71090.7586-0.31820.25560.683-0.54460.928640.26546.32315.86
22.8801-0.32821.75982.80710.63326.4102-0.4099-0.65980.4461-0.07410.4003-0.0164-0.1734-0.62740.00960.22010.1201-0.11340.50820.06520.184833.94237.93923.472
33.22040.36911.31135.21981.8494.4806-0.50880.37940.6115-0.97320.16790.5235-0.6996-0.58680.3410.9311-0.098-0.42520.69550.35320.368920.83741.922-5.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 44
2X-RAY DIFFRACTION2B48 - 253
3X-RAY DIFFRACTION3C1 - 264

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