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- PDB-4i4y: BEL beta-trefoil complex with T-Antigen -

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Basic information

Entry
Database: PDB / ID: 4i4y
TitleBEL beta-trefoil complex with T-Antigen
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 / SERINE / BEL-beta trefoil
Function and homology information
Biological speciesBoletus edulis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.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.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_atom_id_1 / _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.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)69,93817
Polymers66,8864
Non-polymers3,05313
Water6,882382
1
A: BEL beta-trefoil
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0309
Polymers33,4432
Non-polymers1,5877
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)34,9088
Polymers33,4432
Non-polymers1,4656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 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
4
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1877
Polymers16,7211
Non-polymers1,4656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2103
Polymers16,7211
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6985
Polymers16,7211
Non-polymers9774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.390, 70.110, 71.520
Angle α, β, γ (deg.)90.00, 106.67, 90.00
Int Tables number4
Space group name H-MP1211

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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: 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.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam 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
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
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: Nov 25, 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: 1.9→30 Å / Num. all: 48087 / Num. obs: 48087 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.35 / % possible all: 96.1

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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: 1.9→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.336 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22541 2421 5 %RANDOM
Rwork0.19065 ---
all0.1924 45649 --
obs0.1924 45649 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.595 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.23 Å2
2--0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 200 382 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025140
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9717027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05623.673275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951537
X-RAY DIFFRACTIONr_chiral_restr0.0790.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214097
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 184 -
Rwork0.249 3209 -
obs--95.74 %
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)
11.0398-0.1112-0.10160.74790.12760.7965-0.0022-0.02880.0067-0.02630.0191-0.06320.02040.0069-0.01690.0481-0.0038-0.00950.0041-0.01080.045317.6629-1.357215.2378
21.01310.0394-0.05390.83840.04070.7147-0.0062-0.0032-0.00160.0276-0.00560.08140.0075-0.0340.01170.04440.00030.0010.0164-0.01020.0354-12.02761.802417.9912
30.8617-0.1369-0.23590.8418-0.0360.867-0.00730.03220.01710.01860.02330.0348-0.0124-0.0571-0.01610.05460.0066-0.00650.0174-0.00050.0205-6.125535.795818.4303
41.4934-0.0388-0.12690.8234-0.04770.90920.0011-0.00380.0057-0.0537-0.0133-0.06190.00740.07430.01220.02970.00850.00440.0132-0.00240.039623.563232.248719.9371
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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