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- PDB-1y2x: Crystal structure of the tetragonal form of the common edible mus... -

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Basic information

Entry
Database: PDB / ID: 1y2x
TitleCrystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine
Componentslectin
KeywordsSUGAR BINDING PROTEIN / ABL / Agaricus bisporus / lectin / mushroom / T-antigen
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
SERINE / : / Agaricus bisporus lectin
Similarity search - Component
Biological speciesAgaricus bisporus (button mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsCarrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: The Antineoplastic Lectin of the Common Edible Mushroom (Agaricus bisporus) Has Two Binding Sites, Each Specific for a Different Configuration at a Single Epimeric Hydroxyl
Authors: Carrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray study of the common edible mushroom (Agaricus bisporus) lectin
Authors: Carrizo, M.E. / Irazoqui, F.J. / Lardone, R.D. / Nores, G.A. / Curtino, J.A. / Capaldi, S. / Perduca, M. / Monaco, H.L.
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / 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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lectin
B: lectin
C: lectin
D: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,11816
Polymers64,2794
Non-polymers2,83912
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-17 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.675, 85.675, 257.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
lectin


Mass: 16069.765 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Agaricus bisporus (button mushroom) / References: GenBank: 606960, UniProt: Q00022*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.7 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, lithium sulfate, isopropanol, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 18, 2004 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 40259 / Num. obs: 40259 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rsym value: 0.079 / Net I/σ(I): 5.5
Reflection shellResolution: 2.36→2.44 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.167 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF UNLIGANDED LECTIN

Resolution: 2.36→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.473 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25241 2028 5 %RANDOM
Rwork0.22756 ---
all0.22881 38380 --
obs0.22881 38380 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.36→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 188 62 4790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9576552
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023688
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.21918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3731.52820
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73224552
X-RAY DIFFRACTIONr_scbond_it1.14432008
X-RAY DIFFRACTIONr_scangle_it1.8534.52000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.359→2.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 155
Rwork0.263 2721

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