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

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Basic information

Entry
Database: PDB / ID: 7aux
TitleCrystal structure of OXA-48 beta-lactamase in the complex with the inhbitor ID2
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 activity / beta-lactamase / response to antibiotic / metal ion binding
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-LKW / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 3, 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)57,0065
Polymers56,1962
Non-polymers8103
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.410, 72.630, 125.660
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 carboxylated (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-LKW / 6-(4-carboxyphenyl)-3-(4-ethylphenyl)-2~{H}-pyrazolo[3,4-b]pyridine-4-carboxylic acid


Mass: 387.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 12% PEG8000, 8% 1-butanol, OXA-48 8.0-8.5 mg/ml, inhibitor/protein 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: 2.05→62.882 Å / Num. obs: 40846 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.2
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2728 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.05→62.882 Å / FOM work R set: 0.8009 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 2010 4.93 %
Rwork0.2061 38760 -
obs0.208 40770 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.01 Å2 / Biso mean: 34.92 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: final / Resolution: 2.05→62.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 58 252 4276
Biso mean--53.58 45.04 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084122
X-RAY DIFFRACTIONf_angle_d1.1475584
X-RAY DIFFRACTIONf_chiral_restr0.042578
X-RAY DIFFRACTIONf_plane_restr0.005716
X-RAY DIFFRACTIONf_dihedral_angle_d15.2341516
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.10130.31221430.2962272898
2.1013-2.15810.33211400.2684273898
2.1581-2.22160.27931350.265270698
2.2216-2.29330.31711430.2628272497
2.2933-2.37530.2971420.254273697
2.3753-2.47040.31191400.2466264195
2.4704-2.58280.33411420.237275998
2.5828-2.7190.24591460.2335273498
2.719-2.88940.29831390.2304281799
2.8894-3.11240.27341400.2182276298
3.1124-3.42560.26021490.2006277598
3.4256-3.92130.20321480.1793284099
3.9213-4.94010.16451460.1592282098
4.9401-100.21981570.1688298098

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