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- PDB-3qdv: Structure of the orthorhombic form of the Boletus edulis lectin i... -

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Basic information

Entry
Database: PDB / ID: 3qdv
TitleStructure of the orthorhombic form of the Boletus edulis lectin in complex with N-acetyl glucosamine and N-acetyl galactosamine
ComponentsBOLETUS EDULIS LECTIN
KeywordsSUGAR BINDING PROTEIN / Boletus edulis / lectin / mushroom / T-antigen disaccharide / N-acetyl glucosamine / N-acetyl galactosamine / Carbohydrate / Sugar Binding
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Fungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Boletus edulis lectin
Similarity search - Component
Biological speciesBoletus edulis (king bolete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBovi, M. / Carrizo, M.E. / Capaldi, S. / Perduca, M. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
CitationJournal: Glycobiology / Year: 2011
Title: Structure of a lectin with antitumoral properties in king bolete (Boletus edulis) mushrooms.
Authors: Bovi, M. / Carrizo, M.E. / Capaldi, S. / Perduca, M. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOLETUS EDULIS LECTIN
B: BOLETUS EDULIS LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5896
Polymers31,7042
Non-polymers8854
Water3,639202
1
A: BOLETUS EDULIS LECTIN
B: BOLETUS EDULIS LECTIN
hetero molecules

A: BOLETUS EDULIS LECTIN
B: BOLETUS EDULIS LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,17712
Polymers63,4074
Non-polymers1,7708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8970 Å2
ΔGint-16 kcal/mol
Surface area22220 Å2
MethodPISA
2
A: BOLETUS EDULIS LECTIN
hetero molecules

A: BOLETUS EDULIS LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5896
Polymers31,7042
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2840 Å2
ΔGint-2 kcal/mol
Surface area13150 Å2
MethodPISA
3
B: BOLETUS EDULIS LECTIN
hetero molecules

B: BOLETUS EDULIS LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5896
Polymers31,7042
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2810 Å2
ΔGint-3 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.040, 97.446, 84.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 142 / Label seq-ID: 143

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

#1: Protein BOLETUS EDULIS LECTIN


Mass: 15851.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (king bolete) / References: UniProt: F2Z266*PLUS
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.05 M MES, 10% dioxane, 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: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→33.6 Å / Num. obs: 67738 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QDW

3qdw


Resolution: 1.3→33.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.385 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19124 3433 5.1 %RANDOM
Rwork0.17801 ---
obs0.17869 64211 98.27 %-
all-64211 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 60 202 2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9623190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7423.208106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5511516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211770
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3641.51404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31722270
X-RAY DIFFRACTIONr_scbond_it3.8933946
X-RAY DIFFRACTIONr_scangle_it5.5494.5920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeWeight position
11A7X-RAY DIFFRACTIONTIGHT POSITIONAL0.05
11A7X-RAY DIFFRACTIONTIGHT THERMAL0.5
11B7X-RAY DIFFRACTIONTIGHT POSITIONAL0.05
11B7X-RAY DIFFRACTIONTIGHT THERMAL0.5
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 210 -
Rwork0.214 4116 -
obs--85.48 %
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)
10.23620.08150.01980.54790.00210.22530.00790.0049-0.0286-0.00180.0011-0.01830.02010.0262-0.0090.00460.00580.00170.00760.0030.0081-15.941-11.5411-3.9348
20.29880.208-0.05920.5835-0.03860.1852-0.0160.04130.0179-0.00510.024-0.0243-0.0163-0.0567-0.00810.00650.0066-0.00330.0245-0.0010.0098-46.446410.914-5.5023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 145
2X-RAY DIFFRACTION2B0 - 145

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