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

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Basic information

Entry
Database: PDB / ID: 7oln
TitleStructure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Bacterial lectin / Fucosides / Blood group antigen / Human oligosaccharide
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 / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBermeo, R. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 France
CitationJournal: To Be Published
Title: Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen
Authors: Bermeo, R. / Varrot, A.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8492
Polymers14,0111
Non-polymers8381
Water1,74797
1
AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5466
Polymers42,0333
Non-polymers2,5133
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 area6220 Å2
ΔGint-48 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.887, 42.887, 310.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-202-

HOH

21AAA-203-

HOH

31AAA-219-

HOH

41AAA-260-

HOH

51AAA-285-

HOH

61AAA-294-

HOH

71AAA-295-

HOH

81AAA-296-

HOH

91AAA-297-

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: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1-3/a3-b1_b3-c1_b4-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
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: 1.92→36.88 Å / Num. obs: 8958 / % possible obs: 100 % / Redundancy: 15.6 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 23.8
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 601 / CC1/2: 0.982 / Rpim(I) all: 0.143 / Rrim(I) all: 0.424 / % 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: 1.92→36.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.876 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1934 429 4.79 %
Rwork0.152 8528 -
all0.154 --
obs-8957 99.922 %
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: 27.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.066 Å20.033 Å2-0 Å2
2--0.066 Å2-0 Å2
3----0.214 Å2
Refinement stepCycle: LAST / Resolution: 1.92→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 57 97 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131066
X-RAY DIFFRACTIONr_bond_other_d0.0010.017992
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.7211466
X-RAY DIFFRACTIONr_angle_other_deg1.5491.6372299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15522.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89315146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.001153
X-RAY DIFFRACTIONr_chiral_restr0.4310.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021152
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02219
X-RAY DIFFRACTIONr_nbd_refined0.1990.2140
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.2854
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.214
X-RAY DIFFRACTIONr_nbd_other0.2040.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_mcbond_it3.3232.641535
X-RAY DIFFRACTIONr_mcbond_other3.3212.635534
X-RAY DIFFRACTIONr_mcangle_it4.5283.938667
X-RAY DIFFRACTIONr_mcangle_other4.5253.945668
X-RAY DIFFRACTIONr_scbond_it4.3893.104530
X-RAY DIFFRACTIONr_scbond_other4.3883.104530
X-RAY DIFFRACTIONr_scangle_it6.3984.526799
X-RAY DIFFRACTIONr_scangle_other6.3944.532800
X-RAY DIFFRACTIONr_lrange_it8.70233.4711098
X-RAY DIFFRACTIONr_lrange_other8.57433.1781081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.23350.153611X-RAY DIFFRACTION99.8454
1.97-2.0240.285250.177598X-RAY DIFFRACTION100
2.024-2.0830.219290.177586X-RAY DIFFRACTION100
2.083-2.1470.138260.152581X-RAY DIFFRACTION100
2.147-2.2170.252410.168519X-RAY DIFFRACTION100
2.217-2.2950.189260.161527X-RAY DIFFRACTION100
2.295-2.3810.201260.163542X-RAY DIFFRACTION100
2.381-2.4780.238360.168479X-RAY DIFFRACTION100
2.478-2.5890.202200.162467X-RAY DIFFRACTION100
2.589-2.7150.254230.174467X-RAY DIFFRACTION100
2.715-2.8620.209200.151456X-RAY DIFFRACTION100
2.862-3.0350.18130.144416X-RAY DIFFRACTION100
3.035-3.2440.22160.149399X-RAY DIFFRACTION100
3.244-3.5040.194240.145358X-RAY DIFFRACTION99.7389
3.504-3.8380.209150.133348X-RAY DIFFRACTION100
3.838-4.290.129150.116320X-RAY DIFFRACTION99.7024
4.29-4.9530.176110.103281X-RAY DIFFRACTION100
4.953-6.0620.093130.15243X-RAY DIFFRACTION99.6109
6.062-8.5590.155100.188200X-RAY DIFFRACTION100
8.559-36.880.36250.258130X-RAY DIFFRACTION97.8261

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