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- PDB-1onk: Mistletoe lectin I from viscum album -

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Basic information

Entry
Database: PDB / ID: 1onk
TitleMistletoe lectin I from viscum album
Components
  • Beta-galactoside specific lectin I A chain
  • Galactose specific lectin I B chain
Keywordshydrolase/sugar binding protein / RIBOSOME-INACTIVATING PROTEIN TYPE II / hydrolase-sugar binding protein COMPLEX
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
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 ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / PHOSPHATE ION / Beta-galactoside-specific lectin 1 / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabdoulkhakov, A.G. / Savoshkina, Y. / Krauspenhaar, R. / Stoeva, S. / Konareva, N. / Kornilov, V. / Kornev, A.N. / Voelter, W. / Nikonov, S.V. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Mistletoe lectin I from viscum album
Authors: Gabdoulkhakov, A.G. / Savoshkina, Y. / Krauspenhaar, R. / Stoeva, S. / Konareva, N. / Kornilov, V. / Kornev, A.N. / Voelter, W. / Nikonov, S.V. / Betzel, C. / Mikhailov, A.M.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: Beta-galactoside specific lectin I A chain
B: Galactose specific lectin I B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,10522
Polymers57,4522
Non-polymers1,65220
Water6,143341
1
A: Beta-galactoside specific lectin I A chain
B: Galactose specific lectin I B chain
hetero molecules

A: Beta-galactoside specific lectin I A chain
B: Galactose specific lectin I B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,20944
Polymers114,9054
Non-polymers3,30540
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-11 kcal/mol
Surface area20380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.285, 107.285, 311.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: X,X-Y,5/6-Z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-galactoside specific lectin I A chain / RIBOSOME-INACTIVATING PROTEIN TYPE II / MLA


Mass: 28503.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446, rRNA N-glycosylase
#2: Protein Galactose specific lectin I B chain / RIBOSOME-INACTIVATING PROTEIN TYPE II / MLB


Mass: 28949.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81830, UniProt: P81446*PLUS

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Sugars , 1 types, 2 molecules

#6: 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.: 2
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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Non-polymers , 4 types, 359 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: N3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.39 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 40% saturated ammonium sulphate, 30% glycerol in 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2001
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 400080 / Num. obs: 60505 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 46.14 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.056 / Net I/σ(I): 16.05
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.396 / Num. unique all: 3869 / % possible all: 93

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MLL

2mll


Resolution: 2.1→8 Å / Num. parameters: 40089 / Num. restraintsaints: 49383 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 2601 -RANDOM
Rwork0.1598 ---
all0.1629 49599 --
obs0.1629 49599 94.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4454
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 108 341 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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