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- PDB-8bro: Structure of the N-terminal domain of BC2L-C lectin (1-131) in co... -

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Basic information

Entry
Database: PDB / ID: 8bro
TitleStructure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-fucosylamide
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / fucosylamides / antiadhesive drug
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-R7E / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVarrot, A. / Lunstrom, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581European Union
CitationJournal: Molecules / Year: 2023
Title: Identification of New L-Fucosyl and L-Galactosyl Amides as Glycomimetic Ligands of TNF Lectin Domain of BC2L-C from Burkholderia cenocepacia.
Authors: Mazzotta, S. / Antonini, G. / Vasile, F. / Gillon, E. / Lundstrom, J. / Varrot, A. / Belvisi, L. / Bernardi, A.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3732
Polymers14,0111
Non-polymers3621
Water2,198122
1
A: Lectin
hetero molecules

A: Lectin
hetero molecules

A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1206
Polymers42,0333
Non-polymers1,0873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5820 Å2
ΔGint-36 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.008, 43.008, 94.217
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
11A-303-

HOH

21A-325-

HOH

31A-388-

HOH

41A-415-

HOH

51A-420-

HOH

61A-421-

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 (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-R7E / 5-[3-(aminomethyl)phenyl]-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide / (5-(3'-aminomethyl)phenyl)furan-2-carboxamido-b-L-fucopyranose


Mass: 362.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 31.74 % / Description: cube
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: 1.2M Tri sodium citrate ph 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→37.25 Å / Num. obs: 14192 / % possible obs: 99.1 % / Redundancy: 5.6 % / CC1/2: 0.0998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 17.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 716 / CC1/2: 0.888 / Rpim(I) all: 0.297 / Rrim(I) all: 0.54 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→37.246 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.139 / SU B: 1.289 / SU ML: 0.046 / Average fsc free: 0.9785 / Average fsc work: 0.9838 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1687 734 5.172 %
Rwork0.1424 13457 -
all0.144 --
obs-14191 98.94 %
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: 10.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.147 Å20.074 Å2-0 Å2
2--0.147 Å20 Å2
3----0.477 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 26 122 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121047
X-RAY DIFFRACTIONr_bond_other_d0.0040.016955
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.6391440
X-RAY DIFFRACTIONr_angle_other_deg0.6441.5532219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.0954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32810146
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4381032
X-RAY DIFFRACTIONr_chiral_restr0.1030.2172
X-RAY DIFFRACTIONr_chiral_restr_other0.0880.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.2080.2135
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2847
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2510
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.28
X-RAY DIFFRACTIONr_nbd_other0.1780.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.240
X-RAY DIFFRACTIONr_mcbond_it1.5161.046546
X-RAY DIFFRACTIONr_mcbond_other1.521.045546
X-RAY DIFFRACTIONr_mcangle_it2.2751.563686
X-RAY DIFFRACTIONr_mcangle_other2.2861.57687
X-RAY DIFFRACTIONr_scbond_it2.6671.175501
X-RAY DIFFRACTIONr_scbond_other2.6651.175502
X-RAY DIFFRACTIONr_scangle_it3.6971.7754
X-RAY DIFFRACTIONr_scangle_other3.6941.7755
X-RAY DIFFRACTIONr_lrange_it5.61618.6351140
X-RAY DIFFRACTIONr_lrange_other5.25415.551103
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
1.55-1.590.359640.29610060.29910730.9380.95199.72040.247
1.59-1.6340.284670.2199400.22310090.9680.97299.80180.188
1.634-1.6810.21650.2029410.20210080.9770.97399.80160.173
1.681-1.7330.191450.1469320.1489790.9790.98699.79570.129
1.733-1.790.14350.138920.1319310.9870.98999.57040.119
1.79-1.8520.141440.1318700.1329190.9860.98999.45590.123
1.852-1.9220.136400.1258250.1268720.9860.9999.19730.119
1.922-20.137400.1248020.1258440.9890.99199.7630.121
2-2.0890.132420.127670.1218120.9880.99199.63050.119
2.089-2.1910.124280.1267420.1267770.9910.99199.09910.125
2.191-2.3090.177520.1296830.1327420.9790.9999.05660.131
2.309-2.4480.181360.1426580.1447010.9840.98899.00140.143
2.448-2.6160.192270.1446090.1466480.9770.98898.14810.145
2.616-2.8250.165320.1325750.1336210.9810.98997.74560.136
2.825-3.0930.153160.1385490.1385740.9830.98798.43210.144
3.093-3.4550.128320.1294650.1295100.990.98997.4510.139
3.455-3.9830.138330.1284140.1294590.9890.98997.38560.144
3.983-4.8650.191160.1243490.1263840.9850.99195.05210.135
4.865-6.8220.235140.152750.1532990.9830.98896.65550.163
6.822-37.2460.11360.1661630.1641800.9830.9893.88890.181

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