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- PDB-9kl2: Crystal structure of Pleurocybella porrigens lectin (PPL) in comp... -

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Basic information

Entry
Database: PDB / ID: 9kl2
TitleCrystal structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / trefoil / lectin
Function / homologyRicin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / 2-acetamido-2-deoxy-alpha-D-galactopyranose / NITRATE ION / Lectin
Function and homology information
Biological speciesPleurocybella porrigens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAdachi, D. / Ishimoto, N. / Kawabata, H. / Mizutani, K. / Park, S.-Y. / Tame, J.R.H. / Kamata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Institute for Fermentation, OsakaY-2023-2-046 Japan
CitationJournal: To Be Published
Title: Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from Pleurocybella porrigens.
Authors: Adachi, D. / Ishimoto, N. / Mizutani, K. / Takahashi, K. / Kawabata, H. / Park, S.-Y. / Vandebroek, L. / Voet, A.R.D. / Ishiwata, R. / Hayashi, R. / Yamada, M. / Ozeki, Y. / Fujii, Y. / Tame, J.R.H. / Kamata, K.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
C: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7259
Polymers43,8753
Non-polymers8506
Water2,720151
1
A: Lectin
B: Lectin
C: Lectin
hetero molecules

A: Lectin
B: Lectin
C: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,45018
Polymers87,7516
Non-polymers1,69912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)52.762, 221.166, 112.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lectin


Mass: 14625.118 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurocybella porrigens (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: B6ZK51
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.15M Tris, pH 9.5, 4.0M sodium nitrate, 20mM GalNAc

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.03 Å / Num. obs: 44856 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.016 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 3276 / CC1/2: 0.993 / Rpim(I) all: 0.082 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.03 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2213 5.09 %
Rwork0.2284 --
obs0.2295 43514 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 57 151 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.463
X-RAY DIFFRACTIONf_dihedral_angle_d11.5251118
X-RAY DIFFRACTIONf_chiral_restr0.044503
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.30461440.23932597X-RAY DIFFRACTION99
2.04-2.090.37651660.26272555X-RAY DIFFRACTION98
2.09-2.140.28141260.22822618X-RAY DIFFRACTION99
2.14-2.20.28961450.24672589X-RAY DIFFRACTION98
2.2-2.270.3491250.27932415X-RAY DIFFRACTION91
2.27-2.340.29881390.25232403X-RAY DIFFRACTION92
2.34-2.420.3271210.24372528X-RAY DIFFRACTION95
2.42-2.520.28951310.25542545X-RAY DIFFRACTION96
2.52-2.630.24711270.26942570X-RAY DIFFRACTION97
2.63-2.770.31591430.29222544X-RAY DIFFRACTION96
2.77-2.950.32021360.28342560X-RAY DIFFRACTION96
2.95-3.170.23181350.27922565X-RAY DIFFRACTION97
3.17-3.490.27861440.25372623X-RAY DIFFRACTION97
3.49-40.19261560.19652633X-RAY DIFFRACTION99
4-5.040.17521380.1512701X-RAY DIFFRACTION99
5.04-50.030.19031370.18872855X-RAY DIFFRACTION99

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