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- PDB-3zdv: Crystal structure of the LecB lectin from Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 3zdv
TitleCrystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsSUGAR BINDING PROTEIN / GLYCOMIMETIC / INHIBITOR
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / 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
2,4,6-trimethylbenzenesulfonamide / methyl alpha-D-mannopyranoside / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsHauck, D. / Joachim, I. / Frommeyer, B. / Varrot, A. / Philipp, B. / MOller, H.M. / Imberty, A. / Exner, T.E. / Titz, A.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes.
Authors: Hauck, D. / Joachim, I. / Frommeyer, B. / Varrot, A. / Philipp, B. / Moller, H.M. / Imberty, A. / Exner, T.E. / Titz, A.
History
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Other
Revision 1.2Sep 13, 2017Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.type / _struct.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 1.4Dec 20, 2023Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)49,60823
Polymers47,4644
Non-polymers2,14519
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-146.7 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.530, 76.980, 99.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9988, 0.000386, -0.04921), (0.002836, -0.9979, -0.06538), (-0.04913, -0.06544, 0.9966)9.74, 2.25, 0.408
2given(0.7161, -0.6979, 0.00988), (-0.6976, -0.7161, -0.02205), (0.02247, 0.00889, -0.999)1.835, 4.861, 13.64
3given(-0.7158, 0.6972, 0.399), (0.6978, 0.7119, 0.07878), (0.02649, 0.0842, -0.9961)7.123, -3.486, 13.7

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
FUCOSE-BINDING LECTIN PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5
#3: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 468 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-F1A / 2,4,6-trimethylbenzenesulfonamide


Mass: 199.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13NO2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE N-TERMINAL METHIONINE IS MISSING FROM THE MATURE PROTEIN AND ALL THE NUMBERING HAS BEEN SHIFTED BY ONE

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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: 1.89 Å3/Da / Density % sol: 34.93 % / Description: NONE
Crystal growpH: 6.5
Details: 330 MM SODIUM CACODYLATE PH 6.5 200 MM AMMONIUM SULPHATE 30% PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.41→42.25 Å / Num. obs: 76102 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2
Reflection shellResolution: 1.41→1.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DCQ

3dcq


Resolution: 1.41→42.24 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.632 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED SIDE CHAIN WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14529 3805 5 %RANDOM
Rwork0.1146 ---
obs0.11614 72296 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.41→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 123 453 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023625
X-RAY DIFFRACTIONr_bond_other_d0.010.023341
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9585015
X-RAY DIFFRACTIONr_angle_other_deg1.47537633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.61327.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.81815498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.432158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024431
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02841
X-RAY DIFFRACTIONr_nbd_refined0.2610.21053
X-RAY DIFFRACTIONr_nbd_other0.2040.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21830
X-RAY DIFFRACTIONr_nbtor_other0.0840.22160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.226
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.268
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0330.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.081911
X-RAY DIFFRACTIONr_mcbond_other1.1351.081910
X-RAY DIFFRACTIONr_mcangle_it1.271.6272413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0091.3151714
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.72436966
X-RAY DIFFRACTIONr_sphericity_free17.8795178
X-RAY DIFFRACTIONr_sphericity_bonded4.79857188
LS refinement shellResolution: 1.406→1.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 271 -
Rwork0.166 5154 -
obs--97.24 %

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