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- PDB-4g9n: Crystal structure of the Rhizoctonia solani agglutinin in complex... -

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Basic information

Entry
Database: PDB / ID: 4g9n
TitleCrystal structure of the Rhizoctonia solani agglutinin in complex with N'-acetyl-galactosamine
Componentsagglutinin
KeywordsSUGAR BINDING PROTEIN / Lectin / carbohydrate-binding specificity
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Ricin-type beta-trefoil lectin domain-containing protein
Similarity search - Component
Biological speciesRhizoctonia solani (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsSkamnaki, V.T. / Kantsadi, A.L. / Leonidas, D.D.
CitationJournal: Febs J. / Year: 2013
Title: Structural analysis of the Rhizoctonia solani agglutinin reveals a domain-swapping dimeric assembly.
Authors: Skamnaki, V.T. / Peumans, W.J. / Kantsadi, A.L. / Cubeta, M.A. / Plas, K. / Pakala, S. / Zographos, S.E. / Smagghe, G. / Nierman, W.C. / Van Damme, E.J. / Leonidas, D.D.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: agglutinin
B: agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6305
Polymers30,9662
Non-polymers6643
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-2 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.583, 61.251, 32.839
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein agglutinin /


Mass: 15483.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhizoctonia solani (fungus) / References: UniProt: L8WGI4*PLUS
#2: 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 / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Reservoir: 0.1 M sodium acetate, pH 4.2, 20% v/v PEG8000, 0.2 M sodium chloride, 10 mM sodium citrate, a single native crystal was soaked in a solution of 12.9 mM N'-acetyl-galactosamine ...Details: Reservoir: 0.1 M sodium acetate, pH 4.2, 20% v/v PEG8000, 0.2 M sodium chloride, 10 mM sodium citrate, a single native crystal was soaked in a solution of 12.9 mM N'-acetyl-galactosamine (GalNAc) in reservoir solution for 48 hours, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 18, 2012
RadiationMonochromator: Cu-Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→13.86 Å / Num. all: 13153 / Num. obs: 13153 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.33 % / Biso Wilson estimate: 10.02 Å2 / Rsym value: 0.101 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.37 Å / Mean I/σ(I) obs: 5.8 / Rsym value: 0.254 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
REFMACrefinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4G9M

4g9m


Resolution: 2.2→13.859 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 646 4.91 %
Rwork0.1502 --
obs0.1543 13153 99.88 %
all-13153 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1351 Å20 Å2-1.1153 Å2
2--1.3682 Å2-0 Å2
3---0.767 Å2
Refinement stepCycle: LAST / Resolution: 2.2→13.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 45 262 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072270
X-RAY DIFFRACTIONf_angle_d1.1373097
X-RAY DIFFRACTIONf_dihedral_angle_d13.343811
X-RAY DIFFRACTIONf_chiral_restr0.077359
X-RAY DIFFRACTIONf_plane_restr0.004397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.36920.28481220.16922487X-RAY DIFFRACTION99
2.3692-2.60620.26471140.17442472X-RAY DIFFRACTION100
2.6062-2.98010.28371380.16222528X-RAY DIFFRACTION100
2.9801-3.74230.21711320.13862482X-RAY DIFFRACTION100
3.7423-13.85910.17331400.13052538X-RAY DIFFRACTION100

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