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- PDB-9r0r: Class A CTX-M-14 E166A mutant in complex with Oxacillin at room t... -

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Basic information

Entry
Database: PDB / ID: 9r0r
TitleClass A CTX-M-14 E166A mutant in complex with Oxacillin 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-1S6 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionApr 24, 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)31,3552
Polymers30,9511
Non-polymers4031
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10530 Å2
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-452-

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
Details: Position 1-28 denote signal peptides / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-14, bla_2, SAMEA3512100_05103
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7BGE9, beta-lactamase
#2: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 27980 / % possible obs: 100 % / Redundancy: 43.8 % / Biso Wilson estimate: 20.61 Å2 / CC1/2: 0.861 / CC star: 0.962 / Net I/σ(I): 2.65
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2742 / CC1/2: 0.225 / CC star: 0.606
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: 1.8→39.03 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 1229 5.21 %
Rwork0.2011 22376 -
obs0.2031 23605 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 28 160 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492222
X-RAY DIFFRACTIONf_angle_d0.75713057
X-RAY DIFFRACTIONf_chiral_restr0.0487353
X-RAY DIFFRACTIONf_plane_restr0.0071412
X-RAY DIFFRACTIONf_dihedral_angle_d7.705346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.34041310.29232424X-RAY DIFFRACTION99.8
1.87-1.960.30921360.25312418X-RAY DIFFRACTION99.84
1.96-2.060.26331200.21362445X-RAY DIFFRACTION99.96
2.06-2.190.28191480.20132424X-RAY DIFFRACTION99.96
2.19-2.360.22851510.19862455X-RAY DIFFRACTION100
2.36-2.60.2541360.20112458X-RAY DIFFRACTION99.92
2.6-2.970.24361010.20322529X-RAY DIFFRACTION100
2.97-3.740.24381500.18962514X-RAY DIFFRACTION100
3.74-39.030.19061560.18412709X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -5.67849950172 Å / Origin y: 1.71836185559 Å / Origin z: 19.6772638678 Å
111213212223313233
T0.15836893473 Å20.0415033594367 Å20.0001629188309 Å2-0.109680449681 Å26.65136425567E-5 Å2--0.115237922117 Å2
L0.140135774044 °20.0887939073816 °20.0625452970509 °2-0.433458000515 °20.280572282882 °2--0.774822082655 °2
S0.0210174935867 Å °0.0171833853803 Å °0.00746806786361 Å °-0.133066091219 Å °-0.0398456288418 Å °0.0170295112237 Å °-0.21681037756 Å °-0.15702638712 Å °-0.0224344843814 Å °
Refinement TLS groupSelection details: all

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