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- PDB-5may: STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN P... -

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Basic information

Entry
Database: PDB / ID: 5may
TitleSTRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2-Thiophenesulfonamide-N-(beta-L-fucopyranosyl methyl)
ComponentsFucose-binding lectin PA-IIL
KeywordsSUGAR BINDING PROTEIN / LECTIN / LECB / PSEUDOMONAS AERUGINOSA PA14 / glycoinhibitors
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-L-fucopyranose / N-methyl-2-thiophenesulfonamide / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSommer, R. / Imberty, A. / Titz, A. / Varrot, A.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Glycomimetic, Orally Bioavailable LecB Inhibitors Block Biofilm Formation of Pseudomonas aeruginosa.
Authors: Sommer, R. / Wagner, S. / Rox, K. / Varrot, A. / Hauck, D. / Wamhoff, E.C. / Schreiber, J. / Ryckmans, T. / Brunner, T. / Rademacher, C. / Hartmann, R.W. / Bronstrup, M. / Imberty, A. / Titz, A.
History
DepositionNov 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Fucose-binding lectin PA-IIL
B: Fucose-binding lectin PA-IIL
C: Fucose-binding lectin PA-IIL
D: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,39320
Polymers46,7074
Non-polymers1,68616
Water11,620645
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-137 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.089, 65.520, 109.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Fucose-binding lectin PA-IIL


Mass: 11676.710 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: lecB, PA14_20610 / Plasmid: PRS01.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZE85
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-PK6 / N-methyl-2-thiophenesulfonamide


Mass: 177.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7NO2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.98 % / Description: tile shape
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.8 / Details: 20% PEG6K 0.5M LiCl 0.1M citric acid ph 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97712 Å / Relative weight: 1
ReflectionResolution: 1.65→38.59 Å / Num. obs: 45743 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 7.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/av σ(I): 9.4 / Net I/σ(I): 20.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.1 / CC1/2: 0.835 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDS2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a6q

5a6q


Resolution: 1.65→38.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.468 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2221 4.9 %RANDOM
Rwork0.1346 ---
obs0.13646 43462 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.65→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 88 645 4015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023517
X-RAY DIFFRACTIONr_bond_other_d0.0150.023272
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.944829
X-RAY DIFFRACTIONr_angle_other_deg1.87137463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.06727.647153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64915496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.133154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024265
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02815
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9050.9941882
X-RAY DIFFRACTIONr_mcbond_other0.9040.9941881
X-RAY DIFFRACTIONr_mcangle_it1.3621.4882367
X-RAY DIFFRACTIONr_mcangle_other1.3621.4892368
X-RAY DIFFRACTIONr_scbond_it1.731.1831635
X-RAY DIFFRACTIONr_scbond_other1.7291.1831635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.61.7112462
X-RAY DIFFRACTIONr_long_range_B_refined4.93610.1864346
X-RAY DIFFRACTIONr_long_range_B_other4.3989.1433963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126640.09
12B126640.09
21A127360.07
22C127360.07
31A126940.06
32D126940.06
41B126260.07
42C126260.07
51B124800.07
52D124800.07
61C123860.06
62D123860.06
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 132 -
Rwork0.192 2709 -
obs--84.25 %

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