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- PDB-4hr6: Crystal structure of snake gourd (Trichosanthes anguina) seed lec... -

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Basic information

Entry
Database: PDB / ID: 4hr6
TitleCrystal structure of snake gourd (Trichosanthes anguina) seed lectin, a three chain homologue of type II RIPs
Components(LECTIN) x 3
KeywordsSUGAR BINDING PROTEIN / Type II RIP / Lectin / Beta-Trefoil / Carbohydrate binding / Carbohydrate
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
methyl alpha-D-galactopyranoside / Lectin / Seed lectin
Similarity search - Component
Biological speciesTrichosanthes anguina (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins.
Authors: Manoj, N. / Jeyaprakash, A.A. / Pratap, J.V. / Komath, S.S. / Kenoth, R. / Swamy, M.J. / Vijayan, M.
History
DepositionOct 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4535
Polymers57,0653
Non-polymers3882
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-40 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.081, 102.081, 271.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide LECTIN / SGSL / A alpha


Mass: 4647.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF6*PLUS
#2: Protein LECTIN / SGSL / A beta


Mass: 23129.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8*PLUS
#3: Protein LECTIN / SGSL


Mass: 29288.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8*PLUS
#4: Sugar ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE A/B CAINS ARE DIVIDED DUE TO CLEAVAGE. THE SEQUENCE REFERENCES DO NOT CURRENTLY EXIST.

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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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 400, 80% ammonium sulfate, 10mM methyl D-galactose, 5mM mercaptoethanol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2001
RadiationMonochromator: a double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 40805 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 16.7
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 3.6 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→25.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.189 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22873 1901 5 %RANDOM
Rwork0.18702 ---
obs0.18908 40805 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.23 Å2-0 Å2
2--0.23 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 26 178 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194064
X-RAY DIFFRACTIONr_bond_other_d0.0010.023778
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9525541
X-RAY DIFFRACTIONr_angle_other_deg0.7423.0028649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02525.08187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37615652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5031519
X-RAY DIFFRACTIONr_chiral_restr0.070.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
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_it2.6234.7892041
X-RAY DIFFRACTIONr_mcbond_other2.6234.792040
X-RAY DIFFRACTIONr_mcangle_it4.037.172546
X-RAY DIFFRACTIONr_scbond_it3.0115.0792023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 148 -
Rwork0.262 2648 -
obs--95.75 %

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