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- PDB-7fjh: LecA from Pseudomonas aeruginosa in complex with 4-Phenylbutyryl ... -

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Basic information

Entry
Database: PDB / ID: 7fjh
TitleLecA from Pseudomonas aeruginosa in complex with 4-Phenylbutyryl hydroxamic acid (CAS: 32153-46-1)
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / calcium-binding lectins / glycomimetics
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
N-oxidanyl-4-phenyl-butanamide / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsShanina, S. / Kuhaudomlarp, S. / Siebs, E. / Fuchsberger, F. / Denis, M. / da Silva Figueiredo Celstino Gomes, P. / Clausen, M.H. / Seeberger, P.H. / Rognan, D. / Titz, A. ...Shanina, S. / Kuhaudomlarp, S. / Siebs, E. / Fuchsberger, F. / Denis, M. / da Silva Figueiredo Celstino Gomes, P. / Clausen, M.H. / Seeberger, P.H. / Rognan, D. / Titz, A. / Imberty, A. / Rademacher, C.
Funding support France, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)Ti756/5-1 France
German Research Foundation (DFG)RA1944/7-1 France
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0048 France
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Commun Chem / Year: 2022
Title: Targeting undruggable carbohydrate recognition sites through focused fragment library design.
Authors: Shanina, E. / Kuhaudomlarp, S. / Siebs, E. / Fuchsberger, F.F. / Denis, M. / da Silva Figueiredo Celestino Gomes, P. / Clausen, M.H. / Seeberger, P.H. / Rognan, D. / Titz, A. / Imberty, A. / Rademacher, C.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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)51,59910
Polymers51,0814
Non-polymers5196
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-28 kcal/mol
Surface area19390 Å2
Unit cell
Length a, b, c (Å)48.978, 51.678, 160.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: SER / End label comp-ID: SER / Refine code: 0 / 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 / LecA / PA-IL / Galactose-binding lectin


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097
#2: Chemical ChemComp-4R9 / N-oxidanyl-4-phenyl-butanamide


Mass: 179.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG6000, 1 M LiCl, 100 mM sodium acetate pH4 with 20 mM ligand

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.79→46.89 Å / Num. obs: 39017 / % possible obs: 99.4 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.027 / Rrim(I) all: 0.078 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.79-1.837.50.7171539120540.9490.2750.7712.289.9
8.96-46.856.80.04225953830.9960.0160.04535.599.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.79→46.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.678 / SU ML: 0.108 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 2019 5.2 %RANDOM
Rwork0.1801 ---
obs0.1822 36926 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.84 Å2 / Biso mean: 32.245 Å2 / Biso min: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å20 Å2
2--4.53 Å2-0 Å2
3----3.55 Å2
Refinement stepCycle: final / Resolution: 1.79→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 30 223 3835
Biso mean--38.4 37.91 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133708
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173358
X-RAY DIFFRACTIONr_angle_refined_deg1.561.635072
X-RAY DIFFRACTIONr_angle_other_deg1.4071.587708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8575482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98624.793169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.489158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02868
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35330.09
12B35330.09
21A35660.08
22C35660.08
31A35070.11
32D35070.11
41B35680.07
42C35680.07
51B35270.09
52D35270.09
61C35590.09
62D35590.09
LS refinement shellResolution: 1.792→1.839 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 129 -
Rwork0.305 2481 -
all-2610 -
obs--91.87 %

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