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

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Basic information

Entry
Database: PDB / ID: 5maz
TitleSTRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 3-Thiophenesulfonamide-2,5-dimethyl-N-methyl-beta-L-fucopyranoside
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,2,5-trimethyl-3-thiophenesulfonamide / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSommer, R. / Imberty, A. / Titz, A. / Varrot, A.
Funding support1items
OrganizationGrant numberCountry
COSTCOST-STSM-ECOST-STSM-BM1003-240314-042549
CitationJournal: To Be Published
Title: Discovery of a new class of C-glycoside based inhibitors of the virulence factor LecB from Pseudomonas aeruginosa
Authors: Sommer, R. / Wagner, S. / Varrot, A. / Hauk, D. / Ryckmans, T. / Hartman, R.W. / Brunner, T. / Rademacher, C. / Imberty, A. / Titz, A.
History
DepositionNov 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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)48,65922
Polymers46,7074
Non-polymers1,95318
Water11,818656
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-133 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.881, 49.881, 288.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
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

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Protein / Sugars , 2 types, 8 molecules ABCD

#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)
Gene: lecB, PA14_20610 / Plasmid: PRS01.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZE85
#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

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Non-polymers , 5 types, 670 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IGF / N,2,5-trimethyl-3-thiophenesulfonamide


Mass: 205.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H11NO2S2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.24 Å3/Da / Density % sol: 45.16 % / Description: cluster of rods
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 22% PEG8K 50 mM AMSO4 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.45→37.07 Å / Num. obs: 71656 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 7.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Net I/av σ(I): 10 / Net I/σ(I): 27.1
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 11 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 7.6 / CC1/2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDS2016data reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a6q

5a6q


Resolution: 1.45→37.07 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.797 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14196 3598 5 %RANDOM
Rwork0.12336 ---
obs0.12434 67895 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.45→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 106 656 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023626
X-RAY DIFFRACTIONr_bond_other_d0.0020.023362
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9475008
X-RAY DIFFRACTIONr_angle_other_deg0.98937687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.39627.707157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.81815510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.389154
X-RAY DIFFRACTIONr_chiral_restr0.1040.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
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_it0.8270.9221940
X-RAY DIFFRACTIONr_mcbond_other0.8270.9221939
X-RAY DIFFRACTIONr_mcangle_it1.2331.3872460
X-RAY DIFFRACTIONr_mcangle_other1.2331.3872461
X-RAY DIFFRACTIONr_scbond_it1.4521.0761686
X-RAY DIFFRACTIONr_scbond_other1.4521.0771686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1081.5642549
X-RAY DIFFRACTIONr_long_range_B_refined4.08913.2293886
X-RAY DIFFRACTIONr_long_range_B_other3.99812.9533846
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)
11A71820.06
12B71820.06
21A70840.06
22C70840.06
31A71080.07
32D71080.07
41B73520.06
42C73520.06
51B73680.08
52D73680.08
61C70980.07
62D70980.07
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 268 -
Rwork0.151 4995 -
obs--99.94 %

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