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

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Basic information

Entry
Database: PDB / ID: 7olw
TitleStructure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-N-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-VJW / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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)14,3592
Polymers14,0111
Non-polymers3481
Water2,486138
1
AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0786
Polymers42,0333
Non-polymers1,0453
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 area6380 Å2
ΔGint-38 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.931, 42.931, 94.882
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-303-

HOH

21AAA-340-

HOH

31AAA-402-

HOH

41AAA-415-

HOH

51AAA-430-

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-VJW / 5-(3-aminophenyl)furan-2-carboxamido-(beta-L-fucopyranose) / 5-(3-aminophenyl)-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide


Mass: 348.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.8 Å3/Da / Density % sol: 31.72 %
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 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.32→47.44 Å / Num. obs: 23283 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Net I/σ(I): 30.6
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 1150 / CC1/2: 0.959 / Rpim(I) all: 0.158 / Rrim(I) all: 0.505 / % possible all: 100

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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: 1.32→37.179 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.986 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.01 / ESU R Free: 0.009
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1293 1163 5.003 %
Rwork0.1032 22083 -
all0.105 --
obs-23246 99.996 %
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: 14.674 Å2
Baniso -1Baniso -2Baniso -3
1-1.987 Å20 Å20 Å2
2--1.987 Å20 Å2
3----3.974 Å2
Refinement stepCycle: LAST / Resolution: 1.32→37.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 25 138 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171048
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6331537
X-RAY DIFFRACTIONr_angle_other_deg1.5441.5722422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5615150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0722.05139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25615164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.751153
X-RAY DIFFRACTIONr_chiral_restr0.0820.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
X-RAY DIFFRACTIONr_nbd_refined0.2060.2168
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2899
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2529
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.216
X-RAY DIFFRACTIONr_nbd_other0.1980.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.228
X-RAY DIFFRACTIONr_mcbond_it1.471.331579
X-RAY DIFFRACTIONr_mcbond_other1.4631.328578
X-RAY DIFFRACTIONr_mcangle_it1.8762.006736
X-RAY DIFFRACTIONr_mcangle_other1.8782.009737
X-RAY DIFFRACTIONr_scbond_it2.091.555535
X-RAY DIFFRACTIONr_scbond_other2.0881.555536
X-RAY DIFFRACTIONr_scangle_it2.5262.24801
X-RAY DIFFRACTIONr_scangle_other2.5252.24802
X-RAY DIFFRACTIONr_lrange_it2.98617.2281191
X-RAY DIFFRACTIONr_lrange_other2.88216.6011165
X-RAY DIFFRACTIONr_rigid_bond_restr2.42332161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3540.191720.121641X-RAY DIFFRACTION100
1.354-1.3910.134900.1051588X-RAY DIFFRACTION100
1.391-1.4320.158650.0891566X-RAY DIFFRACTION100
1.432-1.4760.101740.0881496X-RAY DIFFRACTION100
1.476-1.5240.128540.0791476X-RAY DIFFRACTION100
1.524-1.5780.117720.0761411X-RAY DIFFRACTION100
1.578-1.6370.109890.0791318X-RAY DIFFRACTION100
1.637-1.7040.118710.0731317X-RAY DIFFRACTION100
1.704-1.7790.125620.0791255X-RAY DIFFRACTION100
1.779-1.8660.107790.0911196X-RAY DIFFRACTION100
1.866-1.9670.128530.0931133X-RAY DIFFRACTION100
1.967-2.0860.117510.0931078X-RAY DIFFRACTION100
2.086-2.230.111700.097998X-RAY DIFFRACTION100
2.23-2.4080.131570.102942X-RAY DIFFRACTION100
2.408-2.6370.136360.111884X-RAY DIFFRACTION100
2.637-2.9470.145510.11770X-RAY DIFFRACTION100
2.947-3.4010.099380.107698X-RAY DIFFRACTION100
3.401-4.160.131400.099587X-RAY DIFFRACTION100
4.16-5.8610.132230.126466X-RAY DIFFRACTION100
5.861-37.1790.288160.242263X-RAY DIFFRACTION99.6429

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