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- PDB-4i4u: BEL beta-trefoil complex with galactose -

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Basic information

Entry
Database: PDB / ID: 4i4u
TitleBEL beta-trefoil complex with galactose
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 / alpha-D-galactopyranose / BEL-beta trefoil
Function and homology information
Biological speciesBoletus edulis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 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)68,57114
Polymers66,8864
Non-polymers1,68610
Water10,899605
1
A: BEL beta-trefoil
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4668
Polymers33,4432
Non-polymers1,0236
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)34,1056
Polymers33,4432
Non-polymers6634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2624
Polymers16,7211
Non-polymers5403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2044
Polymers16,7211
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8442
Polymers16,7211
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2624
Polymers16,7211
Non-polymers5403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.400, 70.010, 71.630
Angle α, β, γ (deg.)90.00, 106.57, 90.00
Int Tables number4
Space group name H-MP1211
DetailsC+D

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Components

#1: Protein
BEL beta-trefoil


Mass: 16721.391 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (fungus) / References: UniProt: R4GRU5*PLUS
#2: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 25% PEG4000, 0.2 M 1-butyl-3-methylimidazolium chloride, pH 8.5, 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: Jun 22, 2011
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→27.6 Å / Num. all: 83522 / Num. obs: 83522 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.4
Reflection shellResolution: 1.57→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.1 / % possible all: 87.8

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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: 1.57→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.371 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 4200 5 %RANDOM
Rwork0.19925 ---
all0.20047 79300 --
obs0.20047 79300 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.57→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4755 0 112 605 5472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025042
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9596905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9823.626273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.87615695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8571537
X-RAY DIFFRACTIONr_chiral_restr0.0840.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214033
LS refinement shellResolution: 1.57→1.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 277 -
Rwork0.278 4892 -
obs--80.97 %
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)
10.3951-0.01770.00590.21730.05780.34930.0333-0.0099-0.001-0.0159-0.0047-0.02250.03870.0102-0.02860.03390.007-0.0040.0058-0.00350.006117.2143-1.373415.0776
20.5907-0.1264-0.02250.2109-0.22310.33180.0541-0.00610.0481-0.00750.01470.05170.0214-0.0275-0.06880.0218-0.00710.01140.00770.00510.0296-12.51591.841417.7294
30.591-0.1478-0.06110.16510.08640.47510.00150.01680.00960.00360.03240.03290.0071-0.0224-0.03390.02120.0069-0.00190.01650.01460.0167-5.854435.82718.7349
40.6589-0.0783-0.01030.20650.04240.28270.010.0105-0.0121-0.0025-0.0128-0.0393-0.02660.00220.00280.01770.0041-0.00610.0072-0.00290.013823.923332.164320.0731
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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