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- PDB-7vu9: Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6... -

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Basic information

Entry
Database: PDB / ID: 7vu9
TitlePholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)[GlcNAc(beta1-4)]GlcNAc
ComponentsLectin (PhoSL)
KeywordsSUGAR BINDING PROTEIN / Lectin / Trimer / Fucose
Function / homologyFORMIC ACID / Lectin (PhoSL)
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsYamasaki, K. / Yamasaki, T. / Kubota, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02397 Japan
CitationJournal: Febs J. / Year: 2023
Title: Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection.
Authors: Yamasaki, K. / Adachi, N. / Ngwe Tun, M.M. / Ikeda, A. / Moriya, T. / Kawasaki, M. / Yamasaki, T. / Kubota, T. / Nagashima, I. / Shimizu, H. / Tateno, H. / Morita, K.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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: Lectin (PhoSL)
B: Lectin (PhoSL)
C: Lectin (PhoSL)
D: Lectin (PhoSL)
E: Lectin (PhoSL)
F: Lectin (PhoSL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,34518
Polymers26,6466
Non-polymers3,69912
Water2,774154
1
A: Lectin (PhoSL)
B: Lectin (PhoSL)
C: Lectin (PhoSL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1739
Polymers13,3233
Non-polymers1,8506
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint17 kcal/mol
Surface area6590 Å2
MethodPISA
2
D: Lectin (PhoSL)
E: Lectin (PhoSL)
F: Lectin (PhoSL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1739
Polymers13,3233
Non-polymers1,8506
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint16 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.739, 127.057, 39.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21B-328-

HOH

31D-312-

HOH

41E-321-

HOH

51F-326-

HOH

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Components

#1: Protein/peptide
Lectin (PhoSL)


Mass: 4440.958 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Pholiota squarrosa (fungus) / References: UniProt: A0A384E107
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4.3 M sodium formate (pH 7.0)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.154→44.87 Å / Num. obs: 17730 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.18
Reflection shellResolution: 2.154→2.28 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 5358 / CC1/2: 0.684 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A86

6a86


Resolution: 2.154→44.865 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.909 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2446 887 5.003 %
Rwork0.1788 16842 -
all0.182 --
obs-17729 99.842 %
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: 38.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.064 Å20 Å20 Å2
2---0.041 Å20 Å2
3----0.023 Å2
Refinement stepCycle: LAST / Resolution: 2.154→44.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 252 154 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132230
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181890
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.8183094
X-RAY DIFFRACTIONr_angle_other_deg1.211.7464430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.7125.67261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.724.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83215252
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg26.075154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
X-RAY DIFFRACTIONr_nbd_refined0.1920.2283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21571
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21028
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.215
X-RAY DIFFRACTIONr_nbd_other0.2490.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2710.220
X-RAY DIFFRACTIONr_mcbond_it3.3263.886972
X-RAY DIFFRACTIONr_mcbond_other3.3243.887973
X-RAY DIFFRACTIONr_mcangle_it5.1395.7821208
X-RAY DIFFRACTIONr_mcangle_other5.1385.7861209
X-RAY DIFFRACTIONr_scbond_it4.2064.2851257
X-RAY DIFFRACTIONr_scbond_other4.2084.2851255
X-RAY DIFFRACTIONr_scangle_it6.2436.2741880
X-RAY DIFFRACTIONr_scangle_other6.2426.2741881
X-RAY DIFFRACTIONr_lrange_it7.92345.2662291
X-RAY DIFFRACTIONr_lrange_other7.94345.0792274
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
2.154-2.210.439640.312180.30612930.7670.85599.14930.293
2.21-2.270.353620.28211800.28612440.8090.84199.83920.274
2.27-2.3360.336620.29411670.29712290.8150.8321000.282
2.336-2.4080.383590.28911180.29411780.7690.83699.91510.274
2.408-2.4860.321580.27511040.27811620.8690.8721000.25
2.486-2.5730.341550.23910500.24411050.840.8941000.215
2.573-2.670.295540.22610290.22910830.850.8821000.201
2.67-2.7790.235520.2069940.20810460.9040.911000.183
2.779-2.9020.294500.2029430.2079940.8950.92599.89940.187
2.902-3.0430.289480.2129160.2169640.9130.9321000.198
3.043-3.2070.264450.2048580.2079030.9250.9381000.192
3.207-3.40.26440.1868260.198710.9310.94899.88520.176
3.4-3.6330.264410.1737900.1778320.9320.96199.87980.17
3.633-3.9220.18390.1357320.1377720.9660.9799.87050.138
3.922-4.2940.149350.1156570.1176930.9760.9899.85570.124
4.294-4.7950.184320.0976170.1016490.9690.9851000.109
4.795-5.5260.138290.1145540.1155830.9780.9851000.127
5.526-6.7430.226250.1444700.1474970.9520.97699.59760.147
6.743-9.4290.224200.1723760.1743970.9620.97499.74810.189
9.429-44.8650.273130.1932420.1962580.9310.97198.83720.238

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