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- PDB-2mll: MISTLETOE LECTIN I FROM VISCUM ALBUM -

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Basic information

Entry
Database: PDB / ID: 2mll
TitleMISTLETOE LECTIN I FROM VISCUM ALBUM
Components(PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)) x 2
KeywordsRIBOSOME / RIBOSOME-INACTIVATING PROTEIN TYPE II
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
Beta-galactoside-specific lectin 1 / Beta-galactoside-specific lectin 4
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKrauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T.P. ...Krauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T.P. / Mikhailov, A. / Voelter, W. / Betzel, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 1999
Title: Crystal structure of mistletoe lectin I from Viscum album.
Authors: Krauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T. / Mikhailov, A. / Voelter, W. / Betzel, C.
History
DepositionMar 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 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 1.5Nov 20, 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: PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
B: PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3925
Polymers52,7292
Non-polymers6643
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-4 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.648, 107.648, 311.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

#1: Protein PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)


Mass: 25656.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: Q6ITZ3*PLUS
#2: Protein PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)


Mass: 27072.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81830, UniProt: Q6ITZ3*PLUS
#3: 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.: 3
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3

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Sample preparation

CrystalDensity Matthews: 4.94 Å3/Da / Density % sol: 75.08 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
240-45 %ammonium sulfate1reservoir
30.18 M1reservoirNaCl
40.1 Macetate1reservoiror 0.1M phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 29232 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.025
Reflection shellResolution: 2.7→10 Å / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 334925 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.181

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AAI

2aai


Resolution: 2.7→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.319 -5 %
Rwork0.251 --
all-29232 -
obs-29232 99.1 %
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 42 215 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0660.055
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1720.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor10.73.5
X-RAY DIFFRACTIONp_staggered_tor25.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.320
X-RAY DIFFRACTIONp_special_tor45.415
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS

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