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- PDB-7r55: B-trefoil lectin from Salpingoeca rosetta in complex with Gb3 -

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Basic information

Entry
Database: PDB / ID: 7r55
TitleB-trefoil lectin from Salpingoeca rosetta in complex with Gb3
ComponentsSarol-1
KeywordsSUGAR BINDING PROTEIN / lectin / Gb3 / b-trefoil / pore forming lectin
Function / homologyRicin B-like lectins / Uncharacterized protein
Function and homology information
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
DepositionFeb 10, 2022Deposition 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarol-1
B: Sarol-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1157
Polymers73,0362
Non-polymers2,0805
Water10,881604
1
A: Sarol-1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 37.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,5273
Polymers36,5181
Non-polymers1,0092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sarol-1
hetero molecules


  • defined by author
  • 37.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,5894
Polymers36,5181
Non-polymers1,0713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.341, 58.997, 210.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 4 - 326 / Label seq-ID: 4 - 326

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Sarol-1


Mass: 36517.785 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) / Strain (production host): BL21(DE3) / References: UniProt: F2UID9
#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.403 Å3/Da / Density % sol: 48.84 % / Description: rock
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM amino acids Morpheus I, 35 % PEG SMEAR MEDIUM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.84→45.18 Å / Num. obs: 62904 / % possible obs: 99.8 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.05 / Rrim(I) all: 0.106 / Net I/σ(I): 11.8
Reflection shell

Num. unique obs: 3696 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
9.01-45.147.10.0250.9990.0130.028
1.84-1.887.81.0340.7920.5721.185

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimless1.12.12data scaling
PHASER2.8.3phasing
BUCCANEER0.5.0model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QE4

7qe4


Resolution: 1.84→45.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.174 / SU B: 3.71 / SU ML: 0.108 / Average fsc free: 0.9048 / Average fsc work: 0.9189 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2396 2982 4.747 %
Rwork0.1844 59836 -
all0.187 --
obs-62818 99.755 %
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: 27.838 Å2
Baniso -1Baniso -2Baniso -3
1-2.658 Å2-0 Å20 Å2
2---1.087 Å2-0 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 140 604 5700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0135356
X-RAY DIFFRACTIONr_bond_other_d0.0010.0144803
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.6887341
X-RAY DIFFRACTIONr_angle_other_deg1.4871.60611126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77921.829257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4641532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
X-RAY DIFFRACTIONr_nbd_refined0.1990.2811
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24468
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22509
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2460
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2230.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.231
X-RAY DIFFRACTIONr_nbd_other0.2310.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.252
X-RAY DIFFRACTIONr_mcbond_it3.2142.822669
X-RAY DIFFRACTIONr_mcbond_other3.2142.8182668
X-RAY DIFFRACTIONr_mcangle_it4.0894.2113359
X-RAY DIFFRACTIONr_mcangle_other4.0894.2133360
X-RAY DIFFRACTIONr_scbond_it4.1483.0812687
X-RAY DIFFRACTIONr_scbond_other4.1483.0812687
X-RAY DIFFRACTIONr_scangle_it5.5444.5083982
X-RAY DIFFRACTIONr_scangle_other5.5444.5083983
X-RAY DIFFRACTIONr_lrange_it6.74833.5395633
X-RAY DIFFRACTIONr_lrange_other6.67333.0645504
X-RAY DIFFRACTIONr_ncsr_local_group_10.1290.059643
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.129240.05007
12BX-RAY DIFFRACTIONLocal ncs0.129240.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.8880.2991990.2994225X-RAY DIFFRACTION97.2949
1.888-1.940.3111960.2614273X-RAY DIFFRACTION100
1.94-1.9960.3031930.2314175X-RAY DIFFRACTION100
1.996-2.0570.2642090.2084069X-RAY DIFFRACTION100
2.057-2.1250.261800.1893916X-RAY DIFFRACTION100
2.125-2.1990.2421830.1783782X-RAY DIFFRACTION100
2.199-2.2820.2472080.1893646X-RAY DIFFRACTION100
2.282-2.3750.2382250.1653467X-RAY DIFFRACTION99.9729
2.375-2.4810.2511670.1753413X-RAY DIFFRACTION100
2.481-2.6020.2681800.173210X-RAY DIFFRACTION100
2.602-2.7430.2621590.1783108X-RAY DIFFRACTION99.9694
2.743-2.9090.2481410.1712919X-RAY DIFFRACTION100
2.909-3.110.2061330.1682775X-RAY DIFFRACTION100
3.11-3.3590.2661200.1912600X-RAY DIFFRACTION99.9632
3.359-3.680.2531090.192399X-RAY DIFFRACTION99.9601
3.68-4.1140.224940.1812210X-RAY DIFFRACTION99.8267
4.114-4.750.174970.1381907X-RAY DIFFRACTION99.6024
4.75-5.8170.168840.1451661X-RAY DIFFRACTION99.8284
5.817-8.2230.253700.1891314X-RAY DIFFRACTION100
8.223-45.180.244350.226767X-RAY DIFFRACTION98.5258

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