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- PDB-2y9f: High-resolution Structural Insights on the Sugar-recognition and ... -

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Basic information

Entry
Database: PDB / ID: 2y9f
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: / 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 / carbohydrate binding / Mainly Beta / Hemolytic lectin LSLa
Function and homology information
Biological speciesLAETIPORUS SULPHUREUS (chicken-of-the-woods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOLYTIC LECTIN LSLA


Theoretical massNumber of molelcules
Total (without water)17,1801
Polymers17,1801
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.580, 59.540, 61.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.74 Å3/Da / Density % sol: 30 % / 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: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→34 Å / Num. obs: 22387 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.4 / % possible all: 98.4

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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: 1.47→30.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.529 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19372 1138 5.1 %RANDOM
Rwork0.15753 ---
obs0.1593 21152 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.192 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.47→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 252 1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3151.951706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71723.01663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72515186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.171158
X-RAY DIFFRACTIONr_chiral_restr0.1790.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021998
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_it1.3391.5744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11521206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2433509
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7584.5500
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: 1.466→1.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 97 -
Rwork0.23 1523 -
obs--97.53 %
Refinement TLS params.Method: refined / Origin x: -0.33 Å / Origin y: 0.28 Å / Origin z: -3.237 Å
111213212223313233
T0.016 Å20.0054 Å20.0026 Å2-0.0224 Å2-0.0015 Å2--0.0026 Å2
L1.4459 °20.2548 °20.0211 °2-1.8099 °2-0.1865 °2--0.8923 °2
S-0.0359 Å °0.0159 Å °0.0298 Å °-0.0162 Å °0.0215 Å °-0.033 Å °-0.0102 Å °0.0008 Å °0.0143 Å °

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