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- PDB-6stn: Three dimensional structure of the giant reed (Arundodonax) lecti... -

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Basic information

Entry
Database: PDB / ID: 6stn
TitleThree dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N-Acetyl glucosamine
ComponentsArundo donax Lectin (ADL)
KeywordsSUGAR BINDING PROTEIN / ADL / Arundo donax lectin / N-Acetyl glucosamine
Biological speciesArundo donax (giant reed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPerduca, M. / Monaco, H.L. / Bovi, M. / Destefanis, L. / Nadali, D. / Fin, L. / Carrizo, M.E.
CitationJournal: Glycobiology / Year: 2021
Title: Three-dimensional structure and properties of the giant reed (Arundo donax) lectin (ADL).
Authors: Perduca, M. / Bovi, M. / Destefanis, L. / Nadali, D. / Fin, L. / Parolini, F. / Sorio, D. / Carrizo, M.E. / Monaco, H.L.
History
DepositionSep 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arundo donax Lectin (ADL)
B: Arundo donax Lectin (ADL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4495
Polymers33,9142
Non-polymers5353
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-22 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 127.550, 45.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Arundo donax Lectin (ADL)


Mass: 16956.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arundo donax (giant reed)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7.5 % in PEG 8000, 10% ethylene glycol and 0.1 M sodium cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→26.13 Å / Num. obs: 42913 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 6198 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X52

2x52


Resolution: 1.75→25.43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.607 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.084
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2031 4.7 %RANDOM
Rwork0.1483 ---
obs0.1503 40867 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.98 Å2 / Biso mean: 30.51 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å2-0 Å2
2--0.44 Å20 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 1.75→25.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 36 226 2512
Biso mean--27.47 33.33 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.022359
X-RAY DIFFRACTIONr_bond_other_d00.021834
X-RAY DIFFRACTIONr_angle_refined_deg0.5811.9683181
X-RAY DIFFRACTIONr_angle_other_deg0.4963.0084344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3585326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5382596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0691510
X-RAY DIFFRACTIONr_chiral_restr0.0440.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0212808
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02478
X-RAY DIFFRACTIONr_rigid_bond_restr11.97334193
X-RAY DIFFRACTIONr_sphericity_free30.1285176
X-RAY DIFFRACTIONr_sphericity_bonded15.12654170
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 133 -
Rwork0.225 2984 -
all-3117 -
obs--99.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9029-0.03780.17821.4686-0.210.64720.06890.1339-0.2851-0.19870.02840.19880.0908-0.0652-0.09730.0405-0.0045-0.06310.0204-0.00940.227926.97433.1030.454
21.7614-0.11890.07950.86180.17760.78420.0619-0.3054-0.14520.10150.01550.01650.06430.0364-0.07740.03340.0063-0.02610.07680.0360.207136.83335.83313.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 170
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B1 - 170
4X-RAY DIFFRACTION2B201

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