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- PDB-3nbc: Clitocybe nebularis ricin B-like lectin (CNL) in complex with lac... -

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Basic information

Entry
Database: PDB / ID: 3nbc
TitleClitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 4.4
ComponentsRicin B-like lectin
KeywordsSUGAR BINDING PROTEIN / Clitocybe nebularis ricin B-like lectin / lactose
Function / homologyRicin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / protein homodimerization activity / Mainly Beta / beta-lactose / Ricin B-like lectin
Function and homology information
Biological speciesClitocybe nebularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsRenko, M. / Pohleven, J. / Sabotic, J. / Kos, J. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from ...Title: Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from basidiomycete C. nebularis
Authors: Pohleven, J. / Renko, M. / Magister, S. / Smith, D.F. / Kunzler, M. / Strukelj, B. / Turk, D. / Kos, J. / Sabotic, J.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin B-like lectin
B: Ricin B-like lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0833
Polymers31,7412
Non-polymers3421
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-12 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.789, 55.898, 112.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ricin B-like lectin


Mass: 15870.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitocybe nebularis (fungus) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZRS9
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.71 Å3/Da / Density % sol: 54.64 % / Mosaicity: 0.326 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.1M Sodium acetate, 29%(v/v) PEG 550 MME, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.033 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2009 / Details: Collimating and focusing, Pt-coated mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionRedundancy: 8.7 % / Av σ(I) over netI: 64.64 / Number: 1549131 / Rmerge(I) obs: 0.046 / Χ2: 1.81 / D res high: 1.01 Å / D res low: 50 Å / Num. obs: 177749 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.745099.310.0331.82210.5
2.182.7410010.0331.75711
1.92.1810010.0431.97513.7
1.731.910010.0561.98218.2
1.61.7399.910.0691.84417.7
1.511.699.610.0832.3437.4
1.431.5199.410.0942.1827.1
1.371.4399.210.1062.1047.1
1.321.3798.910.1172.0887
1.271.3298.610.1272.1297
1.231.2798.510.1382.0986.9
1.21.2398.310.1492.096.9
1.171.297.910.1631.9656.9
1.141.1797.710.1831.7966.9
1.111.1497.510.2091.5556.9
1.091.1197.310.2391.3866.9
1.071.099710.2771.1986.9
1.051.0796.810.3281.0186.7
1.031.0596.410.3610.8936.4
1.011.0394.810.4030.7685.1
ReflectionResolution: 1.01→50 Å / Num. all: 180640 / Num. obs: 177749 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.809 / Net I/σ(I): 17.5
Reflection shellResolution: 1.01→1.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.403 / Num. unique all: 8467 / Χ2: 0.768 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model was partial structure, obtained by iodine SAD phasing of unpublished data set.

Resolution: 1.01→27.95 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.933 / SU B: 0.444 / SU ML: 0.011 / SU R Cruickshank DPI: 0.023 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. The structure was refined also with MAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 8906 5 %RANDOM
Rwork0.157 ---
all0.159 180640 --
obs0.158 177623 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.9 Å2 / Biso mean: 15.61 Å2 / Biso min: 7.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.01→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 23 596 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0510.0222368
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.9623279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4625317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37625.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.03815362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.434159
X-RAY DIFFRACTIONr_chiral_restr0.3190.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211803
X-RAY DIFFRACTIONr_mcbond_it2.1961.51504
X-RAY DIFFRACTIONr_mcangle_it3.26222481
X-RAY DIFFRACTIONr_scbond_it4.5873864
X-RAY DIFFRACTIONr_scangle_it6.4434.5784
X-RAY DIFFRACTIONr_rigid_bond_restr2.28932368
LS refinement shellResolution: 1.01→1.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.616 665 -
Rwork0.604 11853 -
all-12518 -
obs--94.73 %

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