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- PDB-6kbj: Structure of Lectin from Pleurotus ostreatus in complex with malonate -

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Basic information

Entry
Database: PDB / ID: 6kbj
TitleStructure of Lectin from Pleurotus ostreatus in complex with malonate
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Pleurotus ostreatus / Agglutinin / Ca binding / mushroom / fungi
Function / homologymetal ion binding / MALONATE ION / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 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 1.2Nov 13, 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)40,6649
Polymers39,0051
Non-polymers1,6598
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint14 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.477, 152.477, 146.162
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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 6.29 Å3/Da / Density % sol: 80.44 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.9M sodium malonate

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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 15, 2017 / Details: 3.3 Undulator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.18→132 Å / Num. obs: 52573 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 1.036 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.2613.21.67851380.7730.47210.962100
2.26-2.3513.51.20451960.8730.3341.2510.952100
2.35-2.4613.50.91251670.9160.2530.9480.96100
2.46-2.5813.60.6351950.9470.1750.6540.966100
2.58-2.7513.50.37252020.980.1030.3871.007100
2.75-2.9613.50.22652160.9910.0630.2351.085100
2.96-3.2613.50.12952480.9960.0360.1341.13100
3.26-3.7313.40.07152740.9980.020.0741.137100
3.73-4.713.30.06353500.9980.0180.0651.16399.9
4.7-5012.70.03955870.9990.0110.0410.98899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W5N

5w5n


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.767 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1406 2.9 %RANDOM
Rwork0.1884 ---
obs0.1891 47300 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.86 Å2 / Biso mean: 34.541 Å2 / Biso min: 18.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 107 192 2817
Biso mean--69.44 47.85 -
Num. residues----339
LS refinement shellResolution: 2.2→2.253 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.235 59 -
Rwork-2017 -
obs--55.35 %

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