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- PDB-7aw5: Crystal structure of OXA-48 beta-lactamase in the complex with th... -

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Basic information

Entry
Database: PDB / ID: 7aw5
TitleCrystal structure of OXA-48 beta-lactamase in the complex with the inhibitor ID3
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D Beta-lactamase / OXA-48 / antibiotic / dimer
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-LKH / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D. / Garofalo, B. / Ombrato, R.
CitationJournal: Pharmaceuticals / Year: 2021
Title: Discovery of Novel Chemical Series of OXA-48 beta-Lactamase Inhibitors by High-Throughput Screening.
Authors: Garofalo, B. / Prati, F. / Buonfiglio, R. / Coletta, I. / D'Atanasio, N. / Molteni, A. / Carettoni, D. / Wanke, V. / Pochetti, G. / Montanari, R. / Capelli, D. / Milanese, C. / Di Giorgio, F.P. / Ombrato, R.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9495
Polymers56,1962
Non-polymers7533
Water11,025612
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 73.680, 124.790
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: 28097.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the Lysin 73 is caboxylated (KCX) / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LKH / 4-[(~{E})-[3-(4-chlorophenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]iminomethyl]benzoic acid


Mass: 358.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11ClN4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes, pH 7.5, 12% PEG8000, 8% 1-butanol, OXA-48 8.0-8.5 mg/ml, inhibitor/protein ratio 6.5:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.65→51.67 Å / Num. obs: 80899 / % possible obs: 99.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.38 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 3950 / CC1/2: 0.916

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.65→51.667 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2008 2.49 %
Rwork0.1763 78757 -
obs0.177 80765 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.84 Å2 / Biso mean: 21.26 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.65→51.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 49 630 4636
Biso mean--42.43 33.14 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094101
X-RAY DIFFRACTIONf_angle_d1.1565552
X-RAY DIFFRACTIONf_chiral_restr0.045577
X-RAY DIFFRACTIONf_plane_restr0.005714
X-RAY DIFFRACTIONf_dihedral_angle_d15.0351502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.69120.22651410.21525550100
1.6912-1.7370.19571350.19575528100
1.737-1.78810.24141470.1898552499
1.7881-1.84580.19211420.18045604100
1.8458-1.91180.21651440.18315571100
1.9118-1.98830.211450.18045574100
1.9883-2.07880.23461360.18775593100
2.0788-2.18840.1941420.18175588100
2.1884-2.32550.24861400.17895608100
2.3255-2.50510.24271460.1855626100
2.5051-2.75710.20561400.1865644100
2.7571-3.1560.20091470.18345684100
3.156-3.97610.20011480.16195715100
3.9761-100.18251550.15845948100

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