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- PDB-6z6c: Crystal structurel of FleA lectin in complex with a monovalent in... -

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Basic information

Entry
Database: PDB / ID: 6z6c
TitleCrystal structurel of FleA lectin in complex with a monovalent inhibitor
ComponentsFucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / antiadhesive / fucose binding
Function / homologyadhesion of symbiont to host cell surface via host glycoprotein / Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / TRIETHYLENE GLYCOL / Chem-Q9Q / Fucose-specific lectin
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVarrot, A.
CitationJournal: Org.Biomol.Chem. / Year: 2021
Title: Hexavalent thiofucosides to probe the role of the Aspergillus fumigatus lectin FleA in fungal pathogenicity.
Authors: Dussouy, C. / Lalys, P.A. / Cabanettes, A. / Lehot, V. / Deniaud, D. / Gillon, E. / Balloy, V. / Varrot, A. / Gouin, S.G.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fucose-specific lectin
BBB: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,86515
Polymers69,6152
Non-polymers5,25013
Water12,845713
1
AAA: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6418
Polymers34,8081
Non-polymers2,8337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2247
Polymers34,8081
Non-polymers2,4176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.117, 46.893, 80.173
Angle α, β, γ (deg.)103.083, 98.536, 108.512
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB) / NCS ensembles : (Details: Chains AAA BBB)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Fucose-specific lectin / Aspergillus fumigatus lectin / AFL


Mass: 34807.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: fleA, AFUA_5G14740 / Production host: Escherichia coli KRX (bacteria) / Variant (production host): DE3 / References: UniProt: Q4WW81

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Non-polymers , 5 types, 726 molecules

#2: Chemical
ChemComp-Q9Q / 4-((1-(2-(2-(2-(2-hydroxyethoxy)ethoxy)ethoxy)ethyl)-1H-1,2,3-triazol-4-yl)methoxy)benzyl-a-L-thiofucoside / (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[4-[[1-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]methoxy]p henyl]methylsulfanyl]-6-methyl-oxane-3,4,5-triol


Mass: 543.630 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H37N3O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density meas: 2.2 Mg/m3 / Density % sol: 44 %
Description: clusters of rod broken as single rod for data collection
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 50 mM L-Arginin, 50 mm L-Glutamate, 28% PEG Smear Broad and 5% glycerol (BCS screen 1-32)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.4→42.54 Å / Num. obs: 115240 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 16.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5620 / CC1/2: 0.0963 / Rpim(I) all: 0.236 / Rsym value: 0.388 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AH4

4ah4


Resolution: 1.4→42.534 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.124 / SU B: 2.115 / SU ML: 0.037 / Average fsc free: 0.9572 / Average fsc work: 0.9668 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1579 5702 4.951 %
Rwork0.1185 109477 -
all0.12 --
obs-115179 99.132 %
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: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.957 Å2-0.134 Å20.455 Å2
2---0.471 Å2-0.199 Å2
3----0.277 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 184 713 5806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135362
X-RAY DIFFRACTIONr_bond_other_d0.0030.0184644
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6817331
X-RAY DIFFRACTIONr_angle_other_deg1.5651.61110761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27722.288271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69115749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.221528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026102
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021223
X-RAY DIFFRACTIONr_nbd_refined0.1990.2849
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24466
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22575
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2497
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.214
X-RAY DIFFRACTIONr_nbd_other0.2370.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.233
X-RAY DIFFRACTIONr_mcbond_it2.1041.7342591
X-RAY DIFFRACTIONr_mcbond_other2.0981.7332590
X-RAY DIFFRACTIONr_mcangle_it2.3982.6163258
X-RAY DIFFRACTIONr_mcangle_other2.3992.6163259
X-RAY DIFFRACTIONr_scbond_it2.8912.0192771
X-RAY DIFFRACTIONr_scbond_other2.8912.0192772
X-RAY DIFFRACTIONr_scangle_it3.3582.9324073
X-RAY DIFFRACTIONr_scangle_other3.3572.9324074
X-RAY DIFFRACTIONr_lrange_it3.55521.8576170
X-RAY DIFFRACTIONr_lrange_other3.37721.1655999
X-RAY DIFFRACTIONr_rigid_bond_restr3.999310006
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.0510424
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
1.4-1.4360.2463720.20379330.20586280.8960.90596.25640.194
1.436-1.4760.2193950.17676880.17883630.9250.93796.65190.169
1.476-1.5180.2113840.14975400.15281800.9370.95496.87040.141
1.518-1.5650.1923980.13274180.13579070.9520.96498.84910.125
1.565-1.6160.1853810.11472950.11876960.9570.96999.74010.109
1.616-1.6730.1763600.10570060.10873760.9590.97499.86440.101
1.673-1.7360.1743570.10367930.10771620.9580.97399.83250.1
1.736-1.8070.1553750.09465100.09768890.970.97899.94190.093
1.807-1.8870.1563410.09662190.09965610.9680.97999.98480.097
1.887-1.9790.1683410.10659500.10962930.9650.97799.96820.109
1.979-2.0860.1613320.11156540.11459870.9720.9899.98330.115
2.086-2.2120.1662620.11154070.11456700.970.98299.98240.117
2.212-2.3640.1362600.10351080.10453680.9760.9821000.112
2.364-2.5530.1482120.09747250.09949370.9740.9811000.107
2.553-2.7950.1342640.09943290.10145940.9760.98199.97820.112
2.795-3.1240.1342040.11339300.11441340.9760.9781000.132
3.124-3.6040.1431860.11234710.11436570.9740.981000.133
3.604-4.4060.1331320.11429300.11430620.9780.9821000.141
4.406-6.1980.163910.15622930.15623840.9820.9821000.187
6.198-42.5340.239550.21112770.21313360.9520.95899.70060.258

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