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- PDB-4i4x: BEL beta-trefoil complex with T-Antigen disaccharide -

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Basic information

Entry
Database: PDB / ID: 4i4x
TitleBEL beta-trefoil complex with T-Antigen disaccharide
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 / Thomsen-Friedenreich antigen / BEL beta-trefoil
Function and homology information
Biological speciesBoletus edulis (king bolete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)69,57311
Polymers66,8904
Non-polymers2,6837
Water12,863714
1
A: BEL beta-trefoil
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9786
Polymers33,4452
Non-polymers1,5334
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)34,5955
Polymers33,4452
Non-polymers1,1503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,7221
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8724
Polymers16,7221
Non-polymers1,1503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,7221
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4893
Polymers16,7221
Non-polymers7672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.410, 69.960, 71.790
Angle α, β, γ (deg.)90.00, 106.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BEL beta-trefoil


Mass: 16722.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (king bolete) / References: UniProt: R4GRU9*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 48.58 %
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: 0.9334 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: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. all: 64980 / Num. obs: 64980 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.4
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.3 / % possible all: 95.7

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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: 1.72→25.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.464 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20548 3290 5.1 %RANDOM
Rwork0.17639 ---
all0.17787 61668 --
obs0.17787 61668 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 182 714 5652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025156
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.9767060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29723.577274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.78915705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0341538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214098
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 214 -
Rwork0.207 4343 -
obs--95.02 %
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)
10.80740.0014-0.06150.5957-0.00950.7270.0034-0.0252-0.0031-0.0237-0.0092-0.03680.020.01270.00580.01120.0035-0.0020.0025-0.00240.011817.666-1.356815.2169
20.8392-0.05260.08480.5154-0.0160.64860.0051-0.0258-0.0015-0.0123-0.02220.03330.0113-0.04530.01710.0120.0025-0.00040.0057-0.00440.014-12.07751.875118.0503
30.8115-0.0579-0.25490.70130.07570.6871-0.00030.01790.032-0.00660.01470.03340.0181-0.0313-0.01440.0160.0048-0.00320.00660.00470.0096-5.925835.770918.5983
41.2559-0.1747-0.11170.52570.08890.82490.03420.00490.0317-0.0041-0.0274-0.01050.01350.0601-0.00680.00820.006600.01110.00140.006523.898732.181720.1951
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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