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- PDB-5a6x: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -

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Basic information

Entry
Database: PDB / ID: 5a6x
TitleStructure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with alpha-methyl-fucoside
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsSUGAR BINDING PROTEIN / LECTIN / LECB / PSEUDOMONAS AERUGINOSA PA14
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
methyl alpha-L-fucopyranoside / Fucose-binding lectin PA-IIL / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSommer, R. / Wagner, S. / Varrot, A. / Khaledi, A. / Haussler, S. / Imberty, A. / Titz, A.
CitationJournal: Chem Sci / Year: 2016
Title: The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery.
Authors: Sommer, R. / Wagner, S. / Varrot, A. / Nycholat, C.M. / Khaledi, A. / Haussler, S. / Paulson, J.C. / Imberty, A. / Titz, A.
History
DepositionJul 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 22, 2020Group: Other / Structure summary / Category: audit_author / pdbx_database_status
Item: _audit_author.name / _pdbx_database_status.status_code_sf
Revision 1.3Jul 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_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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.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.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 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
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)47,74016
Polymers46,7074
Non-polymers1,03312
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-139.1 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.558, 65.585, 109.036
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(-0.993, 0.012, 0.116), (-0.006, -0.999, 0.046), (0.117, 0.045, 0.992)27.23, -0.294, -1.75
2given(0.89, 0.442, -0.11), (0.438, -0.897, -0.057), (-0.124, 0.002, -0.992)0.525, -7.048, -14.134
3given(-0.893, -0.449, 0.012), (-0.449, 0.892, -0.041), (0.008, -0.042, -0.999)24.918, 5.391, -16.049

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Components

#1: Protein
FUCOSE-BINDING LECTIN PA-IIL / LECB


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 (bacteria) / Strain: UCBPP-PA14 / Plasmid: PRS01.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U8MRX2, UniProt: A0A0H2ZE85*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL METHIONINE CLEAVED OFF IN THE MATURE PROTEIN SO NUMBERING 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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: NONE
Crystal growpH: 3.8 / Details: 26% PEG 8K 1M LICL 0.1M CITRIC ACID PH 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.92053
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92053 Å / Relative weight: 1
ReflectionResolution: 1.55→37.84 Å / Num. obs: 55470 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A6Q

5a6q


Resolution: 1.55→37.84 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.199 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 2763 5 %RANDOM
Rwork0.12818 ---
obs0.12944 52637 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 56 759 4095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023398
X-RAY DIFFRACTIONr_bond_other_d0.0120.023174
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9324660
X-RAY DIFFRACTIONr_angle_other_deg2.00437242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.24127.838148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.59815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.461152
X-RAY DIFFRACTIONr_chiral_restr0.10.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024094
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02772
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_it0.6940.7071840
X-RAY DIFFRACTIONr_mcbond_other0.6940.7071839
X-RAY DIFFRACTIONr_mcangle_it1.11.0612300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2520.8181558
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 208 -
Rwork0.185 3786 -
obs--98.71 %

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