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

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Basic information

Entry
Database: PDB / ID: 6kbq
TitleCrystal Structure of Lectin from Pleurotus ostreatus in complex with Glycerol
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Pleurotus ostreatus / mushroom / Ca binding protein
Function / homologymetal ion binding / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.299 Å
AuthorsVajravijayan, S. / Pletnev, S. / Luo, Z. / 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
DepositionJun 26, 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 / 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
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)40,72710
Polymers39,0051
Non-polymers1,7229
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint17 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.445, 152.445, 145.762
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#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
#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
#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.: 4 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 6.83 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 1.4M Na2HPO4/K2HPO4, 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: RAYONIX MX300-HS / Detector: CCD / Date: Jun 16, 2017
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.299→30 Å / Num. obs: 44609 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 0.393 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.50.85444220.8360.3620.9290.39499.9
2.38-2.486.30.65843920.8670.2840.7180.40499.8
2.48-2.595.60.45943930.9060.2090.5060.40799.7
2.59-2.736.70.3344280.960.1370.3580.41499.8
2.73-2.96.80.21944210.9830.090.2370.44199.7
2.9-3.126.60.13744290.9910.0570.1490.47199.6
3.12-3.436.30.08244660.9960.0350.090.42399.6
3.43-3.935.80.05244650.9980.0230.0570.36998.9
3.93-4.956.90.0445170.9990.0160.0430.36599
4.95-306.10.03546760.9990.0150.0390.24297.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5N

3w5n


Resolution: 2.299→29.654 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.228 2000 4.48 %
Rwork0.1991 --
obs0.2004 44600 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.74 Å2 / Biso mean: 41.3093 Å2 / Biso min: 26.64 Å2
Refinement stepCycle: final / Resolution: 2.299→29.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 110 74 2702
Biso mean--63.24 40.58 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092702
X-RAY DIFFRACTIONf_angle_d1.0033717
X-RAY DIFFRACTIONf_chiral_restr0.059437
X-RAY DIFFRACTIONf_plane_restr0.008472
X-RAY DIFFRACTIONf_dihedral_angle_d5.9791542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2985-2.3560.27181400.271529993139100
2.356-2.41970.291420.243930063148100
2.4197-2.49080.27471410.246930023143100
2.4908-2.57120.24851410.245430033144100
2.5712-2.6630.26971410.23430013142100
2.663-2.76960.25571420.232130293171100
2.7696-2.89550.25931420.234830123154100
2.8955-3.0480.27191420.224230403182100
3.048-3.23880.23531420.219130303172100
3.2388-3.48850.24451430.20293033317699
3.4885-3.83890.23581430.19093056319999
3.8389-4.39280.18641440.17423068321299
4.3928-5.52870.19481460.15483098324499
5.5287-29.65680.20181510.1843223337497

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