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- PDB-4i4s: BEL beta-trefoil complex with lactose -

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Basic information

Entry
Database: PDB / ID: 4i4s
TitleBEL beta-trefoil complex with lactose
ComponentsBEL beta-trefoil
KeywordsSUGAR BINDING PROTEIN / lectin / fruiting bodies
Function / homologyRicin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / beta-lactose / BEL beta-trefoil
Function and homology information
Biological speciesBoletus edulis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
CitationJournal: Glycobiology / Year: 2013
Title: BEL {beta}-trefoil: A novel lectin with antineoplastic properties in king bolete (Boletus edulis) mushrooms.
Authors: Bovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_assembly_gen / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: BEL beta-trefoil
B: BEL beta-trefoil
C: BEL beta-trefoil
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,18918
Polymers66,6494
Non-polymers2,54014
Water13,457747
1
A: BEL beta-trefoil
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7209
Polymers33,3242
Non-polymers1,3957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: BEL beta-trefoil
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4699
Polymers33,3242
Non-polymers1,1457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2815
Polymers16,6621
Non-polymers6194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4394
Polymers16,6621
Non-polymers7773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9384
Polymers16,6621
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5315
Polymers16,6621
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.050, 39.140, 119.390
Angle α, β, γ (deg.)90.00, 93.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BEL beta-trefoil


Mass: 16662.172 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (fungus) / References: UniProt: R4GRU6*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 5
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M magnesium acetate, 20% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2006
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20.5 Å / Num. all: 131858 / Num. obs: 131858 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.7 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I4P

4i4p


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.587 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20356 6648 5 %RANDOM
Rwork0.18854 ---
all0.1893 125098 --
obs0.1893 125098 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.532 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 169 747 5656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025097
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9636992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.823.913276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.84415668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9371532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214076
LS refinement shellResolution: 1.4→1.433 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 461 -
Rwork0.226 8725 -
obs--98.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.696-0.18550.2540.7453-0.21190.922-0.0106-0.0312-0.0312-0.00950.0420.0443-0.0319-0.0693-0.03140.0020.00350.0030.01220.01370.019610.8191-0.801351.4669
20.7350.0186-0.050.5534-0.02070.80920.0186-0.0585-0.01890.04760.0081-0.0076-0.0226-0.0171-0.02670.01240.00170.00140.01130.01060.013825.7756-2.535477.5941
30.57590.0453-0.00890.5959-0.1440.83420.0098-0.0124-0.00010.04260.00930.0049-0.0198-0.0336-0.0190.01540.01020.00520.00930.00290.0064-4.769416.256122.9274
40.7159-0.05250.13120.58380.00710.98610.0049-0.001-0.0102-0.03670.02080.068-0.0147-0.1218-0.02570.00530.0023-0.00790.02670.01220.0234-18.951818.172-3.6147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2B1 - 146
3X-RAY DIFFRACTION3C1 - 146
4X-RAY DIFFRACTION4D1 - 146

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