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- PDB-9raj: Class A CTX-M-14 E166A mutant in complex with Dicloxacillin at ro... -

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Basic information

Entry
Database: PDB / ID: 9raj
TitleClass A CTX-M-14 E166A mutant in complex with Dicloxacillin at room temperature
ComponentsBeta-lactamase
KeywordsPROTEIN BINDING / Antibiotic resistance / Class A beta-lactamase / isoxazolyl penicillins
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-DXU / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGore, G. / Schulz, E.C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Federal Ministry for Education and Research01KI2114 Germany
CitationJournal: Commun Chem / Year: 2025
Title: Binding mode of Isoxazolyl Penicillins to a Class-A beta-lactamase at ambient conditions.
Authors: Gore, G. / Prester, A. / von Stetten, D. / Bartels, K. / Schulz, E.C.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 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)31,4302
Polymers30,9511
Non-polymers4781
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.150, 42.150, 234.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30951.256 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_p301310
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3H219, beta-lactamase
#2: Chemical ChemComp-DXU / Dicloxacillin, open form / dicloxacillin - open form / (3R,4R,5R)-3-(2,6-dichlorophenyl)-N-{(1R)-1-[(2R,4S)-4-(dihydroxymethyl)-5,5-dimethyl-1,3-thiazolidin-2-yl]-2-oxoethyl}-5-methyl-1,2-oxazolidine-4-carboxamide


Mass: 478.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25Cl2N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 293 K / Method: batch mode
Details: CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch crystallization setups

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→117.65 Å / Num. obs: 27982 / % possible obs: 100 % / Redundancy: 92.8 % / Biso Wilson estimate: 21.03 Å2 / CC1/2: 0.938 / CC star: 0.984 / Net I/σ(I): 4.04
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2734 / CC1/2: 0.535 / CC star: 0.835
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: Hare-Chip , silicon

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→78.07 Å / SU ML: 0.2179 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 1432 5.14 %
Rwork0.1969 26442 -
obs0.1984 27874 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 30 172 2139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612275
X-RAY DIFFRACTIONf_angle_d1.17423142
X-RAY DIFFRACTIONf_chiral_restr0.0758367
X-RAY DIFFRACTIONf_plane_restr0.0079411
X-RAY DIFFRACTIONf_dihedral_angle_d14.8469855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.30561220.29982609X-RAY DIFFRACTION99.82
1.76-1.830.33191540.2862592X-RAY DIFFRACTION99.78
1.83-1.910.29771420.26322566X-RAY DIFFRACTION99.96
1.91-2.020.24311250.20832595X-RAY DIFFRACTION100
2.02-2.140.24341460.21112610X-RAY DIFFRACTION100
2.14-2.310.27021600.19712579X-RAY DIFFRACTION99.93
2.31-2.540.21691440.20232628X-RAY DIFFRACTION99.96
2.54-2.910.19971190.19532685X-RAY DIFFRACTION100
2.91-3.660.25641590.18312701X-RAY DIFFRACTION100
3.66-78.070.16281610.16642877X-RAY DIFFRACTION99.97

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