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- PDB-8ad2: Tobacco lectin Nictaba in complex with triacetylchitotriose -

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Basic information

Entry
Database: PDB / ID: 8ad2
TitleTobacco lectin Nictaba in complex with triacetylchitotriose
ComponentsNictaba
KeywordsSUGAR BINDING PROTEIN / lectin / jelly-roll / NAG-binding / secreted / nuclear
Function / homologyPhloem protein 2-like / Phloem protein 2 / metal ion binding / triacetyl-beta-chitotriose / Nictaba
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Citation
Journal: Glycobiology / Year: 2024
Title: The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode.
Authors: Bloch, Y. / Osterne, V.J.S. / Savvides, S.N. / Van Damme, E.J.M.
#1: Journal: Biorxiv / Year: 2024
Title: The crystal structure of the archetypical Nictaba plant lectin reveals the molecular basis for its carbohydrate-binding properties
Authors: Bloch, Y. / Da Silva Osterne, V.J. / Savvides, S.N. / Van Damme, E.J.M.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nictaba
B: Nictaba
C: Nictaba
D: Nictaba
E: Nictaba
F: Nictaba
G: Nictaba
H: Nictaba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,18536
Polymers153,1358
Non-polymers4,05028
Water12,791710
1
A: Nictaba
B: Nictaba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,96711
Polymers38,2842
Non-polymers1,6839
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nictaba
D: Nictaba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7429
Polymers38,2842
Non-polymers4587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Nictaba
F: Nictaba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,36910
Polymers38,2842
Non-polymers1,0858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Nictaba
H: Nictaba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1086
Polymers38,2842
Non-polymers8244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.660, 146.159, 81.908
Angle α, β, γ (deg.)90.000, 95.874, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Nictaba / Sam1 / Sam2


Mass: 19141.893 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N-terminal Met-Gly and are a cloning scar. / Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: NT1 / Plasmid: pEt28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysIq / References: UniProt: Q94EW1
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM ZnAc, 100 mM ZnCl2, 100 mM Bis-Tris pH 7.5, 20 % Medium smear. Soaked and cryoprotected in ML supplemented with 5% (v/v) glycerol, 5% (v/v) ethylene glycol , 5% (v/v) DMSO, 1 mM triacetylchitotriose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→60.39 Å / Num. obs: 97998 / % possible obs: 93.4 % / Redundancy: 4.06 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.132 / Net I/σ(I): 8.01
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 11697 / CC1/2: 0.51 / Rrim(I) all: 1.109 / % possible all: 69.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER2.8.3phasing
XDS20200131data reduction
XDS20200131data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo

Resolution: 2→54.22 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 2000 2.04 %
Rwork0.1955 95974 -
obs0.1961 97974 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.86 Å2
Refinement stepCycle: LAST / Resolution: 2→54.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10688 0 196 711 11595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013111219
X-RAY DIFFRACTIONf_angle_d1.251315207
X-RAY DIFFRACTIONf_chiral_restr0.07121675
X-RAY DIFFRACTIONf_plane_restr0.00841922
X-RAY DIFFRACTIONf_dihedral_angle_d19.33484159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.3476950.31474589X-RAY DIFFRACTION62.6
2.05-2.110.31781110.2835305X-RAY DIFFRACTION72.69
2.11-2.170.30281300.26916216X-RAY DIFFRACTION85.19
2.17-2.240.30161500.24447215X-RAY DIFFRACTION98.17
2.24-2.320.26371510.23767252X-RAY DIFFRACTION98.76
2.32-2.410.26411520.23217243X-RAY DIFFRACTION98.98
2.41-2.520.27871500.23057232X-RAY DIFFRACTION98.94
2.52-2.650.24851500.21777167X-RAY DIFFRACTION97.64
2.65-2.820.25071520.21457296X-RAY DIFFRACTION99.1
2.82-3.040.24681520.21367307X-RAY DIFFRACTION99.36
3.04-3.340.23651510.18387286X-RAY DIFFRACTION99.28
3.34-3.830.22111520.17047272X-RAY DIFFRACTION99.4
3.83-4.820.16161510.14497295X-RAY DIFFRACTION98.69
4.82-54.220.19331530.18867299X-RAY DIFFRACTION98.18

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