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- PDB-5y42: Native-crystal structure of three chain non-toxic type II ribosom... -

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Basic information

Entry
Database: PDB / ID: 5y42
TitleNative-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina
Components
  • (Seed lectin) x 2
  • Lectin
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
Lectin / Seed lectin
Similarity search - Component
Biological speciesTrichosanthes anguina (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChandran, T. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
SERB, CSIR 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
DepositionJul 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Seed lectin
C: Seed lectin
D: Lectin
E: Seed lectin
F: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3477
Polymers114,1266
Non-polymers2211
Water1,838102
1
A: Lectin
B: Seed lectin
C: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2844
Polymers57,0633
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-45 kcal/mol
Surface area20860 Å2
MethodPISA
2
D: Lectin
E: Seed lectin
F: Seed lectin


Theoretical massNumber of molelcules
Total (without water)57,0633
Polymers57,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-46 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.226, 171.226, 75.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein/peptide Lectin


Mass: 4647.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: N-glycosidase domain / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF6, UniProt: U3KRF8*PLUS
#2: Protein Seed lectin / SGSL


Mass: 23128.002 Da / Num. of mol.: 2 / Fragment: UNP residues 48-253 / 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.: 2 / Fragment: UNP residues 256-519 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8
#4: 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


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.58 % / Description: hexagonal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate monohydrate, 0.1M Tris-Hcl, pH8.5, 30% PEG4000
PH range: 7.4-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 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: 2.9→85.61 Å / Num. obs: 28365 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.198 / Net I/σ(I): 12.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4115 / CC1/2: 0.648 / % 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: 2.9→85.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / SU B: 20.006 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25538 1438 5.1 %RANDOM
Rwork0.20209 ---
obs0.20476 26872 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.28 Å2-0 Å2
2---0.55 Å20 Å2
3---1.79 Å2
Refinement stepCycle: 1 / Resolution: 2.9→85.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 15 102 8126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198190
X-RAY DIFFRACTIONr_bond_other_d0.0020.027359
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.94611156
X-RAY DIFFRACTIONr_angle_other_deg1.077317074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76151016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04424.987391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.497151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081542
X-RAY DIFFRACTIONr_chiral_restr0.1030.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021650
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_it3.9716.0494082
X-RAY DIFFRACTIONr_mcbond_other3.976.0494081
X-RAY DIFFRACTIONr_mcangle_it6.2729.0755092
X-RAY DIFFRACTIONr_mcangle_other6.2719.0745093
X-RAY DIFFRACTIONr_scbond_it4.056.2964108
X-RAY DIFFRACTIONr_scbond_other4.056.2974109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4169.3356065
X-RAY DIFFRACTIONr_long_range_B_refined11.4533619
X-RAY DIFFRACTIONr_long_range_B_other11.4533620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 115 -
Rwork0.336 1952 -
obs--100 %

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