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

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Basic information

Entry
Database: PDB / ID: 6stp
TitleThree dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with sialic acid
ComponentsArundo donax Lectin (ADL)
KeywordsSUGAR BINDING PROTEIN / ADL / Arundo donax lectin / Sialic acid
Function / homologyN-acetyl-alpha-neuraminic acid
Function and homology information
Biological speciesArundo donax (giant reed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.2Oct 23, 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

Downloads & links

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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)34,6255
Polymers33,9142
Non-polymers7113
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-33 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.210, 127.210, 45.370
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-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG 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.: 252 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
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: ID23-1 / Wavelength: 0.91939 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91939 Å / Relative weight: 1
ReflectionResolution: 1.6→63.6 Å / Num. obs: 55614 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3 / Num. unique obs: 8080 / % possible all: 100

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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: 1.6→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.18 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2789 5 %RANDOM
Rwork0.1914 ---
obs0.1922 52733 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.58 Å2 / Biso mean: 36.375 Å2 / Biso min: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 48 252 2550
Biso mean--47.89 36.14 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022371
X-RAY DIFFRACTIONr_bond_other_d00.021838
X-RAY DIFFRACTIONr_angle_refined_deg0.5981.9713201
X-RAY DIFFRACTIONr_angle_other_deg0.4973.0074354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3132596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71915314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0621510
X-RAY DIFFRACTIONr_chiral_restr0.040.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0212816
X-RAY DIFFRACTIONr_gen_planes_other0.010.02478
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 198 -
Rwork0.306 3883 -
all-4081 -
obs--99.78 %
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)
11.4615-0.3631-0.2933.0910.65520.1830.0617-0.14510.20560.0763-0.0116-0.05110.02320.0159-0.050.0381-0.00460.0270.0742-0.04950.4398-15.186-39.8135.886
20.8212-0.70820.01842.39580.04350.31970.13220.11040.0348-0.3018-0.10650.02170.01660.0474-0.02570.0560.03470.03340.0591-0.02470.4063-12.112-49.365-6.607
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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