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- PDB-6li7: Crystal Structure of Lectin from Pleurotus ostreatus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6li7
TitleCrystal Structure of Lectin from Pleurotus ostreatus in complex with GalNAc
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Mushroom Lectin / Pleurotus ostreatus Lectin / Carbohydrate Binding Module / C-type letin / Calcium binding protein
Function / homologymetal ion binding / 2-acetamido-2-deoxy-beta-D-galactopyranose / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsVajravijayan, S. / Pletnev, S. / Luo, Z. / Ankur, T. / Gunasekaran, K. / Nandhagopal, N.
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 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 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)40,7649
Polymers39,0051
Non-polymers1,7598
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint15 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.273, 152.273, 145.975
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-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 226 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.: 222 / 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: 6.26 Å3/Da / Density % sol: 80.36 %
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 X 16M / Detector: PIXEL / Date: Apr 2, 2018
Details: Si 111. Rosenbaum-Rock double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.098→30 Å / Num. obs: 58637 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.996 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 5767 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5N

3w5n


Resolution: 2.098→29.642 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.054 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2055 2000 3.411 %
Rwork0.1927 --
all0.193 --
obs-58628 99.899 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20.003 Å20 Å2
2--0.006 Å2-0 Å2
3----0.019 Å2
Refinement stepCycle: LAST / Resolution: 2.098→29.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 113 222 2840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132695
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172402
X-RAY DIFFRACTIONr_angle_refined_deg2.0981.693699
X-RAY DIFFRACTIONr_angle_other_deg1.4691.615582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4955336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14823.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68815349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.108159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023001
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02544
X-RAY DIFFRACTIONr_nbd_refined0.210.2449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22238
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.21281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_metal_ion_refined0.10.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0690.25
X-RAY DIFFRACTIONr_nbd_other0.1440.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.25
X-RAY DIFFRACTIONr_mcbond_it2.9223.121347
X-RAY DIFFRACTIONr_mcbond_other2.9213.1211346
X-RAY DIFFRACTIONr_mcangle_it3.8614.6671682
X-RAY DIFFRACTIONr_mcangle_other3.864.6671683
X-RAY DIFFRACTIONr_scbond_it4.6013.6491348
X-RAY DIFFRACTIONr_scbond_other4.63.651349
X-RAY DIFFRACTIONr_scangle_it6.2445.3022017
X-RAY DIFFRACTIONr_scangle_other6.2425.3032018
X-RAY DIFFRACTIONr_lrange_it7.48340.0652929
X-RAY DIFFRACTIONr_lrange_other7.30739.462886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.1530.2731460.2614130X-RAY DIFFRACTION99.9766
2.153-2.2120.2641430.2554026X-RAY DIFFRACTION100
2.212-2.2760.2751360.2353886X-RAY DIFFRACTION99.9751
2.276-2.3460.2521360.2373820X-RAY DIFFRACTION99.9242
2.346-2.4230.2561290.2333685X-RAY DIFFRACTION99.9476
2.423-2.5080.2511260.2423559X-RAY DIFFRACTION99.9729
2.508-2.6020.2291220.2233465X-RAY DIFFRACTION100
2.602-2.7090.2031180.2063332X-RAY DIFFRACTION99.971
2.709-2.8290.2241120.2023180X-RAY DIFFRACTION99.9696
2.829-2.9670.2051090.2023079X-RAY DIFFRACTION99.9686
2.967-3.1270.221030.1922917X-RAY DIFFRACTION100
3.127-3.3170.204980.1952784X-RAY DIFFRACTION100
3.317-3.5460.273930.1962613X-RAY DIFFRACTION99.9631
3.546-3.830.179860.1922446X-RAY DIFFRACTION100
3.83-4.1950.158800.1582258X-RAY DIFFRACTION100
4.195-4.6890.135730.1312058X-RAY DIFFRACTION99.4865
4.689-5.4140.152650.1451834X-RAY DIFFRACTION100
5.414-6.6280.188550.1681581X-RAY DIFFRACTION100
6.628-9.3610.178440.1571251X-RAY DIFFRACTION100
9.361-29.50.225260.249724X-RAY DIFFRACTION95.4198

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