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- PDB-7olu: Structure of the N-terminal domain of BC2L-C lectin (1-131) in co... -

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Basic information

Entry
Database: PDB / ID: 7olu
TitleStructure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-C-fucoside ligand
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Bacterial lectin / Fucosides / Glycomimetic / Inhibitor / Anti-microbial
Function / homologyLectin Bc2l-C, N-terminal / : / Bc2l-C, N-terminal domain / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / identical protein binding / Chem-VJT / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.793 Å
AuthorsBermeo, R. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 France
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Targeting a Multidrug-Resistant Pathogen: First Generation Antagonists of Burkholderia cenocepacia 's BC2L-C Lectin.
Authors: Bermeo, R. / Lal, K. / Ruggeri, D. / Lanaro, D. / Mazzotta, S. / Vasile, F. / Imberty, A. / Belvisi, L. / Varrot, A. / Bernardi, A.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3302
Polymers14,0111
Non-polymers3191
Water1,78399
1
AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 43 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)42,9916
Polymers42,0333
Non-polymers9583
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6260 Å2
ΔGint-40 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.954, 43.954, 94.138
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11AAA-302-

HOH

21AAA-340-

HOH

31AAA-387-

HOH

41AAA-399-

HOH

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Components

#1: Protein Lectin


Mass: 14010.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM0185 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EH86
#2: Chemical ChemComp-VJT / (2-(4-(beta-L-fucopyranosylethynyl)phenyl)-2-methylpropan-1-amine / (2~{R},3~{S},4~{R},5~{S},6~{S})-2-[2-[4-(1-azanyl-2-methyl-propan-2-yl)phenyl]ethynyl]-6-methyl-oxane-3,4,5-triol


Mass: 319.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate 1.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→47.07 Å / Num. obs: 9696 / % possible obs: 99.7 % / Redundancy: 20.2 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.013 / Rrim(I) all: 0.041 / Net I/σ(I): 49.1
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 11.1 / Num. unique obs: 563 / CC1/2: 0.99 / Rpim(I) all: 0.077 / Rrim(I) all: 0.241 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wq4

2wq4


Resolution: 1.793→38.065 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.736 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1942 454 4.695 %
Rwork0.1396 9216 -
all0.142 --
obs-9670 99.66 %
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: 25.797 Å2
Baniso -1Baniso -2Baniso -3
1--5.611 Å20 Å2-0 Å2
2---5.611 Å2-0 Å2
3---11.222 Å2
Refinement stepCycle: LAST / Resolution: 1.793→38.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 23 99 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131025
X-RAY DIFFRACTIONr_bond_other_d0.0010.017971
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.641405
X-RAY DIFFRACTIONr_angle_other_deg1.531.572232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1455132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5822.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87915146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.337153
X-RAY DIFFRACTIONr_chiral_restr0.090.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined0.1960.2139
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.2828
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2505
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.212
X-RAY DIFFRACTIONr_nbd_other0.1840.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.218
X-RAY DIFFRACTIONr_mcbond_it2.9832.568531
X-RAY DIFFRACTIONr_mcbond_other2.9722.566530
X-RAY DIFFRACTIONr_mcangle_it4.0233.844662
X-RAY DIFFRACTIONr_mcangle_other4.0213.847663
X-RAY DIFFRACTIONr_scbond_it3.642.819494
X-RAY DIFFRACTIONr_scbond_other3.6382.823495
X-RAY DIFFRACTIONr_scangle_it5.1564.118743
X-RAY DIFFRACTIONr_scangle_other5.1524.122744
X-RAY DIFFRACTIONr_lrange_it6.57831.3451075
X-RAY DIFFRACTIONr_lrange_other6.56431.0361060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.793-1.840.286260.207685X-RAY DIFFRACTION96.2111
1.84-1.890.269290.172647X-RAY DIFFRACTION100
1.89-1.9450.251370.145641X-RAY DIFFRACTION100
1.945-2.0040.235410.147626X-RAY DIFFRACTION100
2.004-2.070.195380.155589X-RAY DIFFRACTION100
2.07-2.1430.223220.149582X-RAY DIFFRACTION100
2.143-2.2230.277220.148586X-RAY DIFFRACTION100
2.223-2.3140.227360.136538X-RAY DIFFRACTION100
2.314-2.4160.206270.141523X-RAY DIFFRACTION100
2.416-2.5340.168240.144497X-RAY DIFFRACTION100
2.534-2.6710.215180.152481X-RAY DIFFRACTION100
2.671-2.8320.207180.163451X-RAY DIFFRACTION99.7872
2.832-3.0270.191180.146431X-RAY DIFFRACTION100
3.027-3.2680.21170.136386X-RAY DIFFRACTION100
3.268-3.5790.178230.131374X-RAY DIFFRACTION100
3.579-3.9980.159150.116338X-RAY DIFFRACTION100
3.998-4.6110.125120.102285X-RAY DIFFRACTION100
4.611-5.6340.24140.11248X-RAY DIFFRACTION100
5.634-7.9110.141130.165194X-RAY DIFFRACTION100
7.911-38.0650.16640.176114X-RAY DIFFRACTION96.7213

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