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

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Basic information

Entry
Database: PDB / ID: 3nbd
TitleClitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 7.1
ComponentsRicin B-like lectin
KeywordsSUGAR BINDING PROTEIN / Clitocybe nebularis ricin B-like lectin / lactose
Function / homology
Function and homology information


carbohydrate binding / protein homodimerization activity
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
alpha-lactose / Ricin B-like lectin
Similarity search - Component
Biological speciesClitocybe nebularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / 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

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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)32,9069
Polymers31,7412
Non-polymers1,1657
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-12 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.119, 85.080, 97.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.82 Å3/Da / Density % sol: 56.4 % / Mosaicity: 0.43 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.085M HEPES sodium, 1.7%(v/v) PEG 400, 2.0M Ammonium sulfate, 19%(w/v) Glycerol, pH 7.1, 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: 8.5 % / Av σ(I) over netI: 48.22 / Number: 1086560 / Rmerge(I) obs: 0.06 / Χ2: 1.73 / D res high: 1.14 Å / D res low: 23 Å / Num. obs: 128514 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.092399.910.0291.6078.8
2.463.0910010.0411.8549.8
2.152.4610010.0662.61115.7
1.952.1510010.0752.48915.3
1.811.9510010.0912.17415.3
1.71.8110010.1092.1310
1.621.710010.1232.1467
1.551.6210010.1342.0056.9
1.491.5510010.1461.7596.9
1.441.4910010.1591.5076.9
1.391.4410010.1741.3566.9
1.351.3910010.1871.2726.8
1.321.3510010.2031.1626.8
1.281.3210010.2171.1186.7
1.251.2810010.2351.0476.7
1.231.2510010.2520.9966.7
1.21.2310010.2690.9356.6
1.181.210010.290.8136.5
1.161.1810010.3110.6616.3
1.141.1665.610.3260.5595
ReflectionResolution: 1.14→23.03 Å / Num. all: 130730 / Num. obs: 128514 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Rmerge(I) obs: 0.06 / Χ2: 1.726 / Net I/σ(I): 11.5
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.326 / Num. unique all: 4260 / Χ2: 0.559 / % possible all: 65.6

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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: 3NBC

3nbc


Resolution: 1.15→23.03 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.156 / WRfactor Rwork: 0.135 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.944 / SU B: 0.608 / SU ML: 0.013 / SU R Cruickshank DPI: 0.028 / SU Rfree: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.029 / 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
Rfree0.16 6458 5 %RANDOM
Rwork0.138 ---
all0.142 130730 --
obs0.139 128492 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.6 Å2 / Biso mean: 15.915 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.15→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 71 535 2844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.050.0412441
X-RAY DIFFRACTIONr_bond_other_d0.0380.0391532
X-RAY DIFFRACTIONr_angle_refined_deg2.2311.9633391
X-RAY DIFFRACTIONr_angle_other_deg1.6892.9973837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5665331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05926.154104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.342158
X-RAY DIFFRACTIONr_chiral_restr0.8160.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
X-RAY DIFFRACTIONr_mcbond_it2.3611.51522
X-RAY DIFFRACTIONr_mcbond_other0.9461.5606
X-RAY DIFFRACTIONr_mcangle_it3.42722514
X-RAY DIFFRACTIONr_scbond_it4.8633919
X-RAY DIFFRACTIONr_scangle_it6.8294.5855
X-RAY DIFFRACTIONr_rigid_bond_restr2.22633973
LS refinement shellResolution: 1.147→1.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 443 -
Rwork0.362 8401 -
all-8844 -
obs--93.66 %

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