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- PDB-7qe3: Se-M variant of B-trefoil lectin from Salpingoeca rosetta in comp... -

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Basic information

Entry
Database: PDB / ID: 7qe3
TitleSe-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc
ComponentsSarol-1
KeywordsSUGAR BINDING PROTEIN / lectin / GalNAc / b-trefoil / pore forming lectin
Function / homologyRicin B-like lectins / (2S)-hexane-1,2,6-triol / 2-acetamido-2-deoxy-beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsNotova, S. / Varrot, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission814029European Union
CitationJournal: Commun Biol / Year: 2022
Title: The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3.
Authors: Notova, S. / Bonnardel, F. / Rosato, F. / Siukstaite, L. / Schwaiger, J. / Lim, J.H. / Bovin, N. / Varrot, A. / Ogawa, Y. / Romer, W. / Lisacek, F. / Imberty, A.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
AAA: Sarol-1
BBB: Sarol-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,49011
Polymers78,4232
Non-polymers1,0669
Water8,107450
1
AAA: Sarol-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6014
Polymers39,2121
Non-polymers3893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Sarol-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8897
Polymers39,2121
Non-polymers6776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.990, 58.579, 166.424
Angle α, β, γ (deg.)90.000, 90.682, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AAABBB

#1: Protein Sarol-1


Mass: 39211.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Strain: ATCC 50818 / BSB-021 / Gene: PTSG_08235 / Plasmid: pET28aTev / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2UID9
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 5 types, 458 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-1JW / (2S)-hexane-1,2,6-triol / (-)-1,2,6-Hexanetriol / 6999990


Mass: 134.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 59.03 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA (Arg, Thr, Lys, His), 45 % precipitant mix 6 Morpheus II-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.2→39.775 Å / Num. obs: 44177 / % possible obs: 99.5 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.072 / Rrim(I) all: 0.12 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3 / Num. unique obs: 3794 / CC1/2: 0.852 / Rpim(I) all: 0.383 / Rrim(I) all: 0.634 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless1.12.2data scaling
XDSdata reduction
SHELXmodel building
SHELXphasing
CRANK2phasing
BUCCANEER1.6.10model building
RefinementMethod to determine structure: MAD / Resolution: 2.2→39.775 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.179 / SU B: 5.354 / SU ML: 0.134 / Average fsc free: 0.9146 / Average fsc work: 0.9327 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2312 2095 4.749 %
Rwork0.1824 42022 -
all0.185 --
obs-44117 99.403 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.486 Å2
Baniso -1Baniso -2Baniso -3
1-0.042 Å20 Å21.775 Å2
2---1.792 Å20 Å2
3---1.708 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 71 450 5504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154785
X-RAY DIFFRACTIONr_angle_refined_deg1.921.6597102
X-RAY DIFFRACTIONr_angle_other_deg1.3721.57811051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8915656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46421.885260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66715783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7721532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined0.1960.2749
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24258
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22391
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.225
X-RAY DIFFRACTIONr_nbd_other0.2150.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.226
X-RAY DIFFRACTIONr_mcbond_it3.5963.1282615
X-RAY DIFFRACTIONr_mcbond_other3.5953.1272614
X-RAY DIFFRACTIONr_mcangle_it5.2014.6743274
X-RAY DIFFRACTIONr_mcangle_other5.2014.6753275
X-RAY DIFFRACTIONr_scbond_it4.5383.5352610
X-RAY DIFFRACTIONr_scbond_other4.5373.5362611
X-RAY DIFFRACTIONr_scangle_it6.8035.1233828
X-RAY DIFFRACTIONr_scangle_other6.8025.1243829
X-RAY DIFFRACTIONr_lrange_it8.5335.425249
X-RAY DIFFRACTIONr_lrange_other8.52535.2615201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.3341620.26331110.26633070.8520.87398.97190.248
2.257-2.3190.3181400.24329530.24731230.8490.88499.03940.229
2.319-2.3860.2491270.2129680.21131180.9040.91299.26230.196
2.386-2.4590.281340.2128260.21429860.890.91399.12930.197
2.459-2.5390.2621300.18627290.18928820.8980.92399.20190.174
2.539-2.6280.2321330.1726770.17328280.9110.93399.36350.157
2.628-2.7270.2511180.16725500.17126850.9070.93599.36690.157
2.727-2.8370.251240.16125020.16526400.9150.94599.46970.152
2.837-2.9630.2311390.16223340.16624820.9290.94699.63740.155
2.963-3.1070.234810.16822910.17123840.9220.94899.49660.162
3.107-3.2730.2521050.18321940.18623070.9180.94799.65320.177
3.273-3.4710.231080.19620760.19821940.9380.94299.54420.192
3.471-3.7080.2181300.17818920.18120270.9480.96199.75330.178
3.708-4.0020.218880.16717850.16918780.9530.96299.73380.168
4.002-4.380.149920.13416640.13517590.9720.97399.82940.139
4.38-4.890.15660.12615450.12716130.9730.97899.8760.133
4.89-5.6320.214880.17713390.17914290.9580.96599.860.183
5.632-6.8630.257470.22611290.22711790.9330.94899.74550.23
6.863-9.5650.233400.2439330.2429730.9280.9461000.252
9.565-39.7750.322430.2795240.2825780.910.92798.09690.296

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