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- PDB-9taz: OXA-48: Q5 mutant in an acyl enzyme complex with piperacillin -

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Open data


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Basic information

Entry
Database: PDB / ID: 9taz
TitleOXA-48: Q5 mutant in an acyl enzyme complex with piperacillin
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / OXA-48 / beta-lactmases / piperacillin / evolution
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
Piperacillin (Open Form) / Hydrolyzed piperacillin / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFrohlich, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Mechanistic Origins and Evolutionary Erosion of Collateral Sensitivity in a beta-lactamase.
Authors: Salamonsen, D. / Buda, K. / Wang, D. / Gulyas, K.V. / van der Kamp, M.W. / Frohlich, C.
History
DepositionNov 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,09910
Polymers28,1891
Non-polymers1,9109
Water3,963220
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,19820
Polymers56,3782
Non-polymers3,82018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3730 Å2
ΔGint-16 kcal/mol
Surface area22200 Å2
Unit cell
Length a, b, c (Å)91.895, 45.340, 64.327
Angle α, β, γ (deg.)90.000, 107.227, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-608-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28188.945 Da / Num. of mol.: 1 / Mutation: A33V, K51E, F72L, S212A, T213A
Source method: isolated from a genetically manipulated source
Details: For GKE and VDSFW no electron density was observed. These amino acids are not displayed in the structure.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-162 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QY24, beta-lactamase

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Non-polymers , 5 types, 229 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-YPP / Hydrolyzed piperacillin / (2R,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 535.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O8S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: See Frohlich et al (2024). Nature Catalysis

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→40.3 Å / Num. obs: 40625 / % possible obs: 99.81 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08011 / Net I/σ(I): 11.42
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.7383 / Num. unique obs: 4031 / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
ABSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.97 Å / SU ML: 0.1658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 3832 4.93 %
Rwork0.1644 73889 -
obs0.1659 40621 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 128 220 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042270
X-RAY DIFFRACTIONf_angle_d1.42783102
X-RAY DIFFRACTIONf_chiral_restr0.0609318
X-RAY DIFFRACTIONf_plane_restr0.0097408
X-RAY DIFFRACTIONf_dihedral_angle_d19.4377351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.25731400.28192708X-RAY DIFFRACTION97.77
1.52-1.540.31041440.2652758X-RAY DIFFRACTION97.74
1.54-1.560.29131410.24152713X-RAY DIFFRACTION98.28
1.56-1.580.27821390.24642759X-RAY DIFFRACTION98.3
1.58-1.610.29621470.24252787X-RAY DIFFRACTION97.67
1.61-1.630.26391390.23562668X-RAY DIFFRACTION98.01
1.63-1.660.23821430.23122730X-RAY DIFFRACTION97.92
1.66-1.690.27611450.21392798X-RAY DIFFRACTION98.69
1.69-1.720.21471440.2132728X-RAY DIFFRACTION98.39
1.72-1.750.2641440.20552780X-RAY DIFFRACTION98.85
1.75-1.790.21861420.20622750X-RAY DIFFRACTION98.1
1.79-1.820.22211420.18782764X-RAY DIFFRACTION98.14
1.82-1.870.2031370.18842715X-RAY DIFFRACTION98.34
1.87-1.910.17811490.1752782X-RAY DIFFRACTION98.16
1.91-1.970.2171430.16822749X-RAY DIFFRACTION98.5
1.97-2.020.19751390.15072756X-RAY DIFFRACTION98.74
2.02-2.090.18421410.1462731X-RAY DIFFRACTION98.56
2.09-2.160.21041450.14672761X-RAY DIFFRACTION98.31
2.16-2.250.1791420.15052726X-RAY DIFFRACTION97.92
2.25-2.350.18271430.14732749X-RAY DIFFRACTION97.67
2.35-2.480.16511340.14682708X-RAY DIFFRACTION97.06
2.48-2.630.19151440.14752726X-RAY DIFFRACTION97.16
2.63-2.830.18181420.14372715X-RAY DIFFRACTION96.42
2.83-3.120.22041400.15282633X-RAY DIFFRACTION96.05
3.12-3.570.16841420.14452740X-RAY DIFFRACTION96.71
3.57-4.490.1531400.12842712X-RAY DIFFRACTION97.74
4.49-22.970.18451410.17442743X-RAY DIFFRACTION97.4

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