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- PDB-5mih: Crystal structure of the lectin LecA from Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 5mih
TitleCrystal structure of the lectin LecA from Pseudomonas aeruginosa in complex with a phenyl-epoxy-galactopyranoside
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / LECTIN / GALACTOSE BINDING PROTEIN / covalent lectin inhibition
Function / homology
Function and homology information


heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-7NU / Chem-ETE / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWagner, S. / Hauk, D. / Hofmann, M. / Joachim, I. / Sommer, R. / Muller, R. / Imberty, A. / Varrot, A. / Titz, A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging.
Authors: Wagner, S. / Hauck, D. / Hoffmann, M. / Sommer, R. / Joachim, I. / Muller, R. / Imberty, A. / Varrot, A. / Titz, A.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / 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_entity_nonpoly.name / _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
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: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,52213
Polymers51,0814
Non-polymers1,4429
Water12,268681
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-4 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.343, 73.771, 101.454
Angle α, β, γ (deg.)90.00, 93.36, 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: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121

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
PA-I galactophilic lectin / PA-IL / Galactose-binding lectin


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N TERMINAL METHIONINE PROCESSED
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lecA, pa1L, PA2570 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-7NU / phenyl 6,7-anhydro-D-glycero-beta-D-galacto-heptopyranoside / Phenyl 6,7-dideoxy-6,7-epoxy-beta-D-galacto-heptopyranoside(6D) / phenyl 6,7-anhydro-D-glycero-beta-D-galacto-heptoside / phenyl 6,7-anhydro-D-glycero-D-galacto-heptoside / phenyl 6,7-anhydro-D-glycero-galacto-heptoside


Type: D-saccharide / Mass: 268.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H16O6
#4: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.01 Å3/Da / Density % sol: 38.74 % / Description: parallelepipoid
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 25% peg 2KMME 100mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.8→27.3 Å / Num. obs: 36960 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/av σ(I): 14.4 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.2 / CC1/2: 0.954 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDS2016data reduction
Aimless0.5.24data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.8→27.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.853 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19362 1907 5.2 %RANDOM
Rwork0.14853 ---
obs0.1509 35035 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.187 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å21.13 Å2
2---1.19 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 94 681 4379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193860
X-RAY DIFFRACTIONr_bond_other_d0.0020.023497
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9475291
X-RAY DIFFRACTIONr_angle_other_deg1.07638047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48325.928167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40115528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.443158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
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_it1.2961.321972
X-RAY DIFFRACTIONr_mcbond_other1.2961.321971
X-RAY DIFFRACTIONr_mcangle_it1.8991.9712472
X-RAY DIFFRACTIONr_mcangle_other1.8981.9712473
X-RAY DIFFRACTIONr_scbond_it1.8411.5311888
X-RAY DIFFRACTIONr_scbond_other1.841.5311889
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8492.2232808
X-RAY DIFFRACTIONr_long_range_B_refined4.46817.5924542
X-RAY DIFFRACTIONr_long_range_B_other4.19716.8114372
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)
11A73700.08
12B73700.08
21A74400.06
22C74400.06
31A73520.09
32D73520.09
41B74640.08
42C74640.08
51B75600.07
52D75600.07
61C73380.08
62D73380.08
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 128 -
Rwork0.198 2531 -
obs--96.76 %

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