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- PDB-4ndu: Crystal structure of L. decastes alpha-galactosyl-binding lectin ... -

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Basic information

Entry
Database: PDB / ID: 4ndu
TitleCrystal structure of L. decastes alpha-galactosyl-binding lectin in complex with alpha-methylgalactoside
ComponentsAlpha-galactosyl-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology: / Alpha-galactosyl binding lectin / galactose binding / methyl alpha-D-galactopyranoside / Alpha-galactosyl-binding lectin
Function and homology information
Biological speciesLyophyllum decastes (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.301 Å
AuthorsVan Eerde, A. / Grahn, E. / Krengel, U.
CitationJournal: Glycobiology / Year: 2015
Title: Atomic-resolution structure of the alpha-galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants.
Authors: van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-galactosyl-binding lectin
B: Alpha-galactosyl-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,5832
Non-polymers3882
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-5 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.098, 75.035, 44.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-galactosyl-binding lectin


Mass: 10291.380 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lyophyllum decastes (fungus) / Organ: fruiting bodies / References: UniProt: A7UNK4
#2: Sugar ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% w/v PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 50871 / Num. obs: 50868 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.44 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.380.6442.2535427797297.2
1.38-1.470.4233.4733701757097.9
1.47-1.590.2515.7831569709398.3
1.59-1.740.1628.7429237656998.9
1.74-1.950.0914.5826612599098.9
1.95-2.240.04825.423523533199.4
2.24-2.740.03433.6520065457599.5
2.74-3.830.02247.715585361099.7
3.830.01854.368756215897.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NDT

4ndt


Resolution: 1.301→18.762 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.14 / σ(F): 1.99 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 2590 5.09 %RANDOM
Rwork0.1732 ---
obs0.1751 50851 98.5 %-
all-50868 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.9 Å2 / Biso mean: 13.3032 Å2 / Biso min: 2.59 Å2
Refinement stepCycle: LAST / Resolution: 1.301→18.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 26 319 1789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111642
X-RAY DIFFRACTIONf_angle_d1.4862233
X-RAY DIFFRACTIONf_chiral_restr0.097232
X-RAY DIFFRACTIONf_plane_restr0.007298
X-RAY DIFFRACTIONf_dihedral_angle_d12.52590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.301-1.32640.30481360.25242578271497
1.3264-1.35340.26221580.21472627278597
1.3534-1.38280.2531510.20212593274497
1.3828-1.4150.29691230.19952655277898
1.415-1.45040.21841320.18242645277798
1.4504-1.48960.23981320.16922631276398
1.4896-1.53340.21951430.16612667281098
1.5334-1.58280.18441370.1522634277199
1.5828-1.63940.20511380.15472680281899
1.6394-1.7050.21231470.15242655280299
1.705-1.78250.18921540.15492670282499
1.7825-1.87640.2161490.16122684283399
1.8764-1.99390.19431430.1662685282899
1.9939-2.14760.19011390.16042709284899
2.1476-2.36340.22221410.16822746288799
2.3634-2.70450.22411420.19252748289099
2.7045-3.4040.20881620.187127722934100
3.404-18.76360.17771630.16042882304599

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