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- PDB-1w3a: Three dimensional structure of a novel pore-forming lectin from t... -

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Basic information

Entry
Database: PDB / ID: 1w3a
TitleThree dimensional structure of a novel pore-forming lectin from the mushroom Laetiporus sulphureus
ComponentsHEMOLYTIC LECTIN LSLA
KeywordsTOXIN/SUGAR BINDING PROTEIN / TOXIN / PORE-FORMING TOXIN / HEMOLYTIC LECTIN / OLIGOMER / BETA-TREFOIL / SUGAR-BINDING PROTEIN / TOXIN-SUGAR BINDING PROTEIN complex
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
: / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Beta Complex / Mainly Beta
Similarity search - Domain/homology
alpha-lactose / Hemolytic lectin LSLa
Similarity search - Component
Biological speciesLAETIPORUS SULPHUREUS (chicken-of-the-woods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.65 Å
AuthorsMancheno, J.M. / Tateno, H. / Goldstein, I.J. / Martinez-Ripoll, M. / Hermoso, J.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Analysis of the Laetiporus Sulphureus Hemolytic Pore-Forming Lectin in Complex with Sugars
Authors: Mancheno, J.M. / Tateno, H. / Goldstein, I.J. / Martinez-Ripoll, M. / Hermoso, J.A.
History
DepositionJul 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 2.1May 8, 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)36,0208
Polymers35,1251
Non-polymers8957
Water1,38777
1
A: HEMOLYTIC LECTIN LSLA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)216,11948
Polymers210,7506
Non-polymers5,36942
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)101.526, 101.526, 193.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein HEMOLYTIC LECTIN LSLA


Mass: 35124.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) LAETIPORUS SULPHUREUS (chicken-of-the-woods)
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.: 1
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 18325 / % possible obs: 99.8 % / Redundancy: 31.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 31.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALEdata scaling
SOLVEphasing
MLPHAREphasing
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.65→14.99 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.27 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 889 5.1 %RANDOM
Rwork0.226 ---
obs0.229 16567 98.5 %-
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: 42.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.65→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 59 77 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212590
X-RAY DIFFRACTIONr_bond_other_d0.0020.022239
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9493521
X-RAY DIFFRACTIONr_angle_other_deg2.05935220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.965311
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_restr0.0840.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022847
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02551
X-RAY DIFFRACTIONr_nbd_refined0.2060.2413
X-RAY DIFFRACTIONr_nbd_other0.2370.22491
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6630.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.51553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31322526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07231036
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9114.5995
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: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 61
Rwork0.3 1168

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