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- PDB-6lik: Crystal Structure of Lectin from Pleurotus ostreatus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6lik
TitleCrystal Structure of Lectin from Pleurotus ostreatus in complex with Galactose
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Pleurotus ostreatus Lectin / Mushroom Lectin / C-type lectin / Calcium mediated sugar binding
Function / homologymetal ion binding / alpha-D-galactopyranose / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsVajravijayan, S. / Pletnev, S. / Luo, Z. / Iqbal, S. / Nandhagopal, N. / Gunasekaran, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Crystallographic and calorimetric analysis on Pleurotus ostreatus lectin and its sugar complexes - promiscuous binding driven by geometry.
Authors: Vajravijayan, S. / Pletnev, S. / Luo, Z. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K.
History
DepositionDec 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7239
Polymers39,0051
Non-polymers1,7188
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint15 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.507, 152.507, 146.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lectin / Lectin 1


Mass: 39004.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pleurotus ostreatus (oyster mushroom) / References: UniProt: E7E2M2

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 125 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 6.29 Å3/Da / Density % sol: 80.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.9M Na2HPO4/K2HPO4, pH 5.5, 33% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 1, 2018 / Details: Si 111
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.4→30.04 Å / Num. obs: 39208 / % possible obs: 98.97 % / Redundancy: 5.1 % / CC1/2: 0.994 / CC star: 0.999 / Rpim(I) all: 0.043 / Rrim(I) all: 0.146 / Net I/σ(I): 12.98
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 3803 / CC1/2: 0.604 / CC star: 0.868 / Rpim(I) all: 0.423

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6kbq

6kbq


Resolution: 2.4→30.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.729 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2000 5.1 %RANDOM
Rwork0.1848 ---
obs0.1862 37149 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.74 Å2 / Biso mean: 36.867 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.4→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 110 121 2736
Biso mean--71.31 44.56 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132692
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172398
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.6883695
X-RAY DIFFRACTIONr_angle_other_deg1.3581.6085574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6145336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39423.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33315349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.149159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
LS refinement shellResolution: 2.402→2.465 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 143 -
Rwork0.286 2649 -
all-2792 -
obs--96.94 %

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