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- PDB-6kc2: Crystal Structure of Lectin from Pleurotus ostreatus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6kc2
TitleCrystal Structure of Lectin from Pleurotus ostreatus in complex with Rhamnose
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Pleurotus ostreatus / mushroom / Ca binding protein
Function / homologymetal ion binding / alpha-L-rhamnopyranose / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.246 Å
AuthorsGunasekaran, K. / Pletnev, S. / Luo, Z. / Vajravijayan, S. / 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 1.2Nov 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)40,6878
Polymers39,0051
Non-polymers1,6827
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint17 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.402, 152.402, 146.035
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: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 6.28 Å3/Da / Density % sol: 80.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.9M 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: 2.25→30 Å / Num. obs: 47965 / % possible obs: 99.7 % / Redundancy: 18.9 % / Biso Wilson estimate: 36.29 Å2 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.042 / Rrim(I) all: 0.185 / Χ2: 0.408 / Net I/σ(I): 3.4 / Num. measured all: 908329
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.3318.41.66946930.8650.3961.7160.37100
2.33-2.4218.31.4147470.8980.3351.450.374100
2.42-2.5316.51.13646940.9040.2841.1720.38299.5
2.53-2.6717.60.77546990.9510.1860.7980.38998.9
2.67-2.8320.90.50547550.9840.1120.5170.397100
2.83-3.0520.90.3147970.9930.0690.3180.422100
3.05-3.3620.50.17647790.9970.040.1810.448100
3.36-3.8519.90.09948420.9990.0230.1020.462100
3.85-4.8417.30.0648370.9990.0150.0620.44599.2
4.84-30190.04651220.9990.0110.0480.37499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5N

3w5n


Resolution: 2.246→29.649 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2000 4.17 %
Rwork0.2028 45912 -
obs0.2036 47912 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.91 Å2 / Biso mean: 36.5817 Å2 / Biso min: 20.2 Å2
Refinement stepCycle: final / Resolution: 2.246→29.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 108 181 2799
Biso mean--58.56 48.55 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122695
X-RAY DIFFRACTIONf_angle_d1.073716
X-RAY DIFFRACTIONf_chiral_restr0.061445
X-RAY DIFFRACTIONf_plane_restr0.007471
X-RAY DIFFRACTIONf_dihedral_angle_d5.871541
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 (%)
2.2455-2.30170.28831380.24723164330298
2.3017-2.36390.25791400.244132193359100
2.3639-2.43340.27291420.244132523394100
2.4334-2.51190.32031410.251932533394100
2.5119-2.60160.2681390.2413174331398
2.6016-2.70570.28041410.227832563397100
2.7057-2.82880.25861420.230132443386100
2.8288-2.97780.29731420.227832733415100
2.9778-3.16410.271430.220832713414100
3.1641-3.40810.23621430.201832953438100
3.4081-3.75050.19541440.195633043448100
3.7505-4.29180.18451460.170533403486100
4.2918-5.40190.1531440.15833316346098
5.4019-29.65120.21031550.202835513706100

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