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- PDB-6zzw: Structure of the N terminal domain of Bc2L-C lectin (1-131) in co... -

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Basic information

Entry
Database: PDB / ID: 6zzw
TitleStructure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) and CAS No 912569-62-1
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / lectins / drug resistance / glycomimetics / anti-adhesive therapy / drug design / fragment based screening
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 / [3-(2-methylimidazol-1-yl)phenyl]methanamine / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLal, K. / Bermeo, R. / Imberty, A. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 France
CitationJournal: Chemistry / Year: 2021
Title: Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia*.
Authors: Lal, K. / Bermeo, R. / Cramer, J. / Vasile, F. / Ernst, B. / Imberty, A. / Bernardi, A. / Varrot, A. / Belvisi, L.
History
DepositionAug 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
C: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,01710
Polymers42,0333
Non-polymers2,9847
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint19 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.459, 42.912, 103.345
Angle α, β, γ (deg.)90.000, 96.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA0 - 1303 - 133
21ALAALABC0 - 1303 - 133
12THRTHRAA0 - 1293 - 132
22THRTHRCB0 - 1293 - 132
13THRTHRBC0 - 1293 - 132
23THRTHRCB0 - 1293 - 132

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ACB

#1: Protein Lectin


Mass: 14010.936 Da / Num. of mol.: 3
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 (E. coli) / References: UniProt: B4EH86

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Sugars , 2 types, 3 molecules

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


Type: oligosaccharide / Mass: 853.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-3DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1-4/a4-b1_b3-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 196 molecules

#4: Chemical ChemComp-QT5 / [3-(2-methylimidazol-1-yl)phenyl]methanamine


Mass: 187.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5.5 mg/ml of protein, 1.2 M sodium citrate, 10 mM ligand at 292 K temperature and cryoprotected with 2.5 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→37.13 Å / Num. obs: 25522 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Rrim(I) all: 0.146 / Net I/σ(I): 10.2 / Num. measured all: 175918 / Scaling rejects: 493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.947.10.5311163316460.8980.2140.573498.1
9.11-37.136.50.06716672570.9970.0280.07316.497.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tig

6tig


Resolution: 1.9→37.13 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.538 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1224 4.8 %RANDOM
Rwork0.1809 ---
obs0.1836 24288 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.73 Å2 / Biso mean: 20.848 Å2 / Biso min: 3.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20.12 Å2
2---1.31 Å20 Å2
3---2.19 Å2
Refinement stepCycle: final / Resolution: 1.9→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 206 206 3293
Biso mean--33.87 26.91 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133170
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172897
X-RAY DIFFRACTIONr_angle_refined_deg1.841.7174359
X-RAY DIFFRACTIONr_angle_other_deg1.4961.6346729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07822.376101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24615421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.999159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023388
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A3775
12B3775
21A3770
22C3770
31B3705
32C3705
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 76 -
Rwork0.234 1821 -
all-1897 -
obs--97.63 %

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