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- PDB-9zot: OXA-23-JDB/PQ-1-219, 30 min complex -

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Basic information

Entry
Database: PDB / ID: 9zot
TitleOXA-23-JDB/PQ-1-219, 30 min complex
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE/INHIBITOR / antibiotic resistance / beta-lactamase / inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsSmith, C.A. / Maggiolo, A.M. / Vakulenko, S.B. / Toth, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01 AI155723 United States
CitationJournal: To Be Published
Title: Potent Inhibition of OXA-23 and Unimpeded Access to PBPs Underpins the Broad Activity of the Novel Carbapenem JDB/PQ-1-219 Against Class D Carbapenemases
Authors: Toth, M. / Stewart, N.K. / Maggiolo, A.M. / Quan, P. / Khan, M.M.K. / Cox, J. / Castro Cabello, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionDec 16, 2025Deposition site: RCSB / Processing site: RCSB
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 OXA-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4423
Polymers31,0121
Non-polymers4312
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.808, 82.808, 86.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

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Components

#1: Protein Beta-lactamase OXA-23


Mass: 31011.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: OXA-23, ari-1, bla-OXA-23, bla_2, bla_3, blaOXA, blaOXA-23, ABUW_0563
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4P2, beta-lactamase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-A1C3I / (2S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-{[(3S)-2,3-dihydroazet-3-yl]sulfanyl}-2-methyl-2H-pyrrole-5-carboxylic acid


Mass: 312.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→38.3 Å / Num. obs: 30951 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.09 / Net I/σ(I): 19.8
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1667 / CC1/2: 0.825 / Rpim(I) all: 0.466

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→38.26 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1565 5.07 %
Rwork0.1766 --
obs0.1778 30878 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 28 113 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072048
X-RAY DIFFRACTIONf_angle_d1.1982771
X-RAY DIFFRACTIONf_dihedral_angle_d19.676784
X-RAY DIFFRACTIONf_chiral_restr0.055308
X-RAY DIFFRACTIONf_plane_restr0.006353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.28971080.26242638X-RAY DIFFRACTION99
1.81-1.870.29361460.27152608X-RAY DIFFRACTION100
1.87-1.950.3121380.24442617X-RAY DIFFRACTION100
1.95-2.030.24161360.18162631X-RAY DIFFRACTION100
2.03-2.140.19861620.17692599X-RAY DIFFRACTION100
2.14-2.280.1961460.17882639X-RAY DIFFRACTION100
2.28-2.450.19411260.1852665X-RAY DIFFRACTION100
2.45-2.70.24091520.1942655X-RAY DIFFRACTION100
2.7-3.090.18081290.18542707X-RAY DIFFRACTION100
3.09-3.890.21051340.16182715X-RAY DIFFRACTION100
3.89-38.260.1591880.15242839X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0333-0.0125-0.0070.22940.13780.0821-0.0508-0.07570.18720.1970.1644-0.1038-0.0527-0.24330.00630.3737-0.00170.00320.33650.06010.232314.708722.59450.0557
22.65790.12170.96810.6407-0.08620.7801-0.02050.19150.041-0.0607-0.010.12590.00620.0017-00.1784-0.0168-0.00660.2458-0.03590.2156-1.459725.528621.7109
32.3613-0.57180.46121.3376-0.57182.04380.07840.4816-0.0829-0.1869-0.05030.05390.1410.09880.00090.17260.006-0.00190.3225-0.03670.23085.329423.317717.0229
41.7372-1.33630.67171.2851-0.60382.6116-0.0273-0.22790.10920.1447-0.01490.1993-0.1614-0.3092-0.00260.17520.00440.01410.2696-0.01150.18035.254327.020734.0732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 208 )
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 273 )

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