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- PDB-6trv: Structure of SapL1 lectin in complex with alpha methyl fucoside -

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Basic information

Entry
Database: PDB / ID: 6trv
TitleStructure of SapL1 lectin in complex with alpha methyl fucoside
ComponentsUncharacterized protein
KeywordsSUGAR BINDING PROTEIN / LECTIN / FUCOSE BINDING / BETA PROPELLER / FUNGAL
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / methyl alpha-L-fucopyranoside / Uncharacterized protein
Function and homology information
Biological speciesScedosporium apiospermum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMartinez Alarcon, D. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
European Commission765581 France
CitationJournal: Sci Rep / Year: 2021
Title: Biochemical and structural studies of target lectin SapL1 from the emerging opportunistic microfungus Scedosporium apiospermum.
Authors: Martinez-Alarcon, D. / Balloy, V. / Bouchara, J.P. / Pieters, R.J. / Varrot, A.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Uncharacterized protein
BBB: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90719
Polymers63,5622
Non-polymers2,34417
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint10 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.064, 45.664, 83.485
Angle α, β, γ (deg.)90.000, 105.054, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 31781.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scedosporium apiospermum (fungus) / Gene: SAPIO_CDS9261 / Cell line (production host): TRX / Production host: Escherichia coli (E. coli) / References: UniProt: A0A084FYP2
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C7H14O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: broken plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M ammonium sulfate (NH4)2SO4 100 mM BICINE pH 8.5 12% Glycerol 10% Glycerol were added for cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→39.99 Å / Num. obs: 21570 / % possible obs: 98.2 % / Redundancy: 2.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.082 / Rsym value: 0.118 / Net I/σ(I): 5.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2212 / CC1/2: 0.7 / Rpim(I) all: 0.417 / Rsym value: 0.598 / % possible all: 98.4

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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: 4D4U

4d4u


Resolution: 2.4→39.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.836 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / ESU R: 0.806 / ESU R Free: 0.285
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2398 1089 5.051 %
Rwork0.175 --
all0.178 --
obs-21561 97.884 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.193 Å2-0 Å21.865 Å2
2---0.899 Å20 Å2
3---0.078 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 155 179 4776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134719
X-RAY DIFFRACTIONr_bond_other_d0.0030.0184145
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.6626446
X-RAY DIFFRACTIONr_angle_other_deg1.4211.6079566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4095586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61521.667228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4441528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025346
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021074
X-RAY DIFFRACTIONr_nbd_refined0.1950.2807
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.24102
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22238
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2203
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0550.22
X-RAY DIFFRACTIONr_nbd_other0.1540.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.26
X-RAY DIFFRACTIONr_mcbond_it3.8733.5662350
X-RAY DIFFRACTIONr_mcbond_other3.8663.5642349
X-RAY DIFFRACTIONr_mcangle_it5.2985.3412934
X-RAY DIFFRACTIONr_mcangle_other5.3015.3432935
X-RAY DIFFRACTIONr_scbond_it4.1833.7022369
X-RAY DIFFRACTIONr_scbond_other4.1753.7022366
X-RAY DIFFRACTIONr_scangle_it5.6745.4633512
X-RAY DIFFRACTIONr_scangle_other5.6785.4633507
X-RAY DIFFRACTIONr_lrange_it6.93540.0455197
X-RAY DIFFRACTIONr_lrange_other6.93440.0485198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.343780.3451475X-RAY DIFFRACTION98.4781
2.462-2.5290.366740.3131489X-RAY DIFFRACTION97.9937
2.529-2.6020.353660.2861406X-RAY DIFFRACTION98.5934
2.602-2.6820.368630.2541399X-RAY DIFFRACTION97.8581
2.682-2.770.313620.2271314X-RAY DIFFRACTION96.8332
2.77-2.8660.295840.1871323X-RAY DIFFRACTION98.6676
2.866-2.9740.243810.1641232X-RAY DIFFRACTION98.8705
2.974-3.0950.25770.161199X-RAY DIFFRACTION98.9915
3.095-3.2310.22620.1561178X-RAY DIFFRACTION99.0415
3.231-3.3880.231610.1641108X-RAY DIFFRACTION98.5666
3.388-3.570.189560.161077X-RAY DIFFRACTION99.0385
3.57-3.7850.229520.1451014X-RAY DIFFRACTION98.4303
3.785-4.0430.182550.12926X-RAY DIFFRACTION97.4181
4.043-4.3640.174420.099861X-RAY DIFFRACTION95.3537
4.364-4.7740.227430.119815X-RAY DIFFRACTION97.3893
4.774-5.3280.19350.147733X-RAY DIFFRACTION96.9697
5.328-6.1350.192350.182644X-RAY DIFFRACTION96.3121
7.469-100.257220.188437X-RAY DIFFRACTION96.0251

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