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- PDB-5a6y: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -

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Entry
Database: PDB / ID: 5a6y
TitleStructure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with mannose-alpha1,3mannoside
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsHYDROLASE / LECTIN / LECB
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
3alpha-alpha-mannobiose / alpha-D-mannopyranose / Fucose-binding lectin PA-IIL / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: Derived calculations / Other / Structure summary / Category: audit_author / pdbx_database_status / struct_conn
Item: _audit_author.name / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
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)48,42318
Polymers46,7074
Non-polymers1,71614
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-128.5 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.979, 49.779, 75.438
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / 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

NCS oper:
IDCodeMatrixVector
1given(0.992, 0.037, 0.12), (0.038, -0.999, -0.003), (0.119, 0.007, -0.993)-3.075, 45.337, 37.625
2given(-0.999, 0.035, -0.031), (0.037, 0.185, -0.982), (-0.029, -0.982, -0.186)3.708, 37.005, 44.991
3given(-0.996, -0.066, -0.066), (-0.052, -0.186, 0.981), (-0.077, 0.98, 0.182)6.661, 8.327, -6.524

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 691 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#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-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNTERMINAL METHIONINE CLEAVED OFF IN THE MATURE PROTEIN SO THE NUMBERING IS 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: 2.13 Å3/Da / Density % sol: 42.38 % / Description: NONE
Crystal growpH: 8.5
Details: 24% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5. 10% GLYCEROL WAS ADDED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.4→44.52 Å / Num. obs: 76843 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.4 / % possible all: 94.9

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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: 1.4→44.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.747 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16328 4016 5.2 %RANDOM
Rwork0.12245 ---
obs0.12457 72808 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.05 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 100 681 4049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023502
X-RAY DIFFRACTIONr_bond_other_d0.0130.023246
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9484822
X-RAY DIFFRACTIONr_angle_other_deg1.80937438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.76427.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24115487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.283151
X-RAY DIFFRACTIONr_chiral_restr0.1130.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024194
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02779
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_it0.8540.7391882
X-RAY DIFFRACTIONr_mcbond_other0.8540.7391881
X-RAY DIFFRACTIONr_mcangle_it0.9841.1122367
X-RAY DIFFRACTIONr_mcangle_other0.9841.1122368
X-RAY DIFFRACTIONr_scbond_it1.1160.8991620
X-RAY DIFFRACTIONr_scbond_other1.1160.8991620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.191.2992455
X-RAY DIFFRACTIONr_long_range_B_refined2.3428.3884296
X-RAY DIFFRACTIONr_long_range_B_other1.7287.0873896
X-RAY DIFFRACTIONr_rigid_bond_restr3.31636748
X-RAY DIFFRACTIONr_sphericity_free17.0425188
X-RAY DIFFRACTIONr_sphericity_bonded3.8557199
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126760.07
12B126760.07
21A124820.08
22C124820.08
31A124920.07
32D124920.07
41B123420.07
42C123420.07
51B123200.07
52D123200.07
61C126980.06
62D126980.06
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 294 -
Rwork0.141 5147 -
obs--96.06 %

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