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- PDB-6uqu: Serendipitous Discovery of Aryl Boronic Acids as beta-Lactamase I... -

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Basic information

Entry
Database: PDB / ID: 6uqu
TitleSerendipitous Discovery of Aryl Boronic Acids as beta-Lactamase Inhibitors
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / boronic acid inhibitors / drug resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYL BORONIC ACID / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.0902 Å
AuthorsScapin, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Serendipitous discovery of aryl boronic acids as beta-lactamase inhibitors.
Authors: Yang, S.W. / Pan, J. / Root, Y. / Scapin, G. / Xiao, L. / Su, J.
History
DepositionOct 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1823
Polymers41,0241
Non-polymers1572
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.993, 71.912, 105.129
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 41024.316 Da / Num. of mol.: 1 / Mutation: R397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, RW109_RW109_01564 / Production host: Escherichia coli (E. coli)
References: UniProt: Q541D8, UniProt: P24735*PLUS, beta-lactamase
#2: Chemical ChemComp-PBC / PHENYL BORONIC ACID / Phenylboronic acid


Mass: 121.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7BO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 10% isopropanol, 100 mM Imidazole, pH=6.5; seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→105.129 Å / Num. obs: 142039 / % possible obs: 100 % / Redundancy: 6.3 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Rsym value: 0.064 / Net I/av σ(I): 8.2 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.092-1.125.90.5081.5103560.2570.6280.50899.8
1.12-1.156.20.4181.8101140.2030.5070.41899.9
1.15-1.186.20.3721.998770.1810.450.372100
1.18-1.226.10.343295830.1680.4170.343100
1.22-1.266.20.2922.492870.1410.3510.292100
1.26-1.36.50.2592.790180.120.3070.259100
1.3-1.356.50.2223.187000.1030.2630.222100
1.35-1.416.30.1853.883790.0880.220.185100
1.41-1.476.40.1474.880440.0690.1750.147100
1.47-1.546.50.1146.277100.0530.1350.114100
1.54-1.636.80.0898.173310.040.1040.089100
1.63-1.736.70.0749.769350.0340.0870.074100
1.73-1.846.40.06111.765730.0280.0720.061100
1.84-1.996.30.05113.860880.0240.060.051100
1.99-2.186.30.04116.956470.0190.0490.041100
2.18-2.446.70.03718.551220.0170.0430.037100
2.44-2.826.50.03320.145630.0150.0380.033100
2.82-3.455.90.03119.438580.0150.0370.03199.8
3.45-4.886.30.02821.530610.0130.0330.028100
4.88-105.1296.30.0318.517930.0140.0350.0399.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.0902→59.35 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.759 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1484 7134 5 %RANDOM
Rwork0.1276 ---
obs0.1286 134800 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 10.517 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---0.13 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.0902→59.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 10 573 3373
Biso mean--8.35 22.78 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192933
X-RAY DIFFRACTIONr_bond_other_d0.0020.022782
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9784001
X-RAY DIFFRACTIONr_angle_other_deg0.94136394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24423.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9621523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_rigid_bond_restr1.72835715
X-RAY DIFFRACTIONr_sphericity_free23.777598
X-RAY DIFFRACTIONr_sphericity_bonded6.23756113
LS refinement shellResolution: 1.091→1.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 483 -
Rwork0.236 9856 -
all-10339 -
obs--99.67 %

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