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- PDB-2y9g: High-resolution Structural Insights on the Sugar-recognition and ... -

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Basic information

Entry
Database: PDB / ID: 2y9g
TitleHigh-resolution Structural Insights on the Sugar-recognition and Fusion Tag Properties of a Versatile b-Trefoil Lectin Domain
ComponentsHEMOLYTIC LECTIN LSLA
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
beta-lactose / alpha-lactose / Hemolytic lectin LSLa
Similarity search - Component
Biological speciesLAETIPORUS SULPHUREUS (chicken-of-the-woods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsAngulo, I. / Acebron, I. / de las Rivas, B. / Munoz, R. / Rodriguez, J.I. / Menendez, M. / Garcia, P. / Tateno, H. / Goldstein, I.J. / Perez-Agote, B. / Mancheno, J.M.
CitationJournal: Glycobiology / Year: 2011
Title: High-Resolution Structural Insights on the Sugar-Recognition and Fusion Tag Properties of a Versatile Beta-Trefoil Lectin Domain from the Mushroom Laetiporus Sulphureus.
Authors: Angulo, I. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Rodriguez-Crespo, I. / Menendez, M. / Garcia, P. / Tateno, H. / Goldstein, I.J. / Perez-Agote, B. / Mancheno, J.M.
History
DepositionFeb 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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: HEMOLYTIC LECTIN LSLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6416
Polymers17,1801
Non-polymers1,4615
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.150, 62.150, 37.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein HEMOLYTIC LECTIN LSLA / LSL-150


Mass: 17180.191 Da / Num. of mol.: 1 / Fragment: B-TREFOIL DOMAIN, RESIDUES 1-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAETIPORUS SULPHUREUS (chicken-of-the-woods)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7Z8V1
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5
Details: 12% (W/V) PEG 4000, 100 MM TRIS-HCL, PH 8.5, 150 MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→53 Å / Num. obs: 18678 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W3A

1w3a


Resolution: 1.67→23.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.287 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 961 5.2 %RANDOM
Rwork0.175 ---
obs0.178 17696 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.67→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 98 262 1557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2492.0771838
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71923.01663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.833158
X-RAY DIFFRACTIONr_chiral_restr0.1850.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021994
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_it0.61.5737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1221195
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4143606
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4024.5642
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 67 -
Rwork0.276 1288 -
obs--96.44 %
Refinement TLS params.Method: refined / Origin x: 14.376 Å / Origin y: 12.85 Å / Origin z: -0.181 Å
111213212223313233
T0.0216 Å2-0.0138 Å20.0045 Å2-0.052 Å20.0007 Å2--0.0234 Å2
L2.4028 °2-0.0386 °20.7824 °2-4.1459 °2-0.1543 °2--2.1061 °2
S-0.0126 Å °0.0191 Å °0.0157 Å °-0.0496 Å °-0.0154 Å °-0.1119 Å °0.0363 Å °0.0717 Å °0.0281 Å °

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