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- PDB-9nt0: OXA-23-meropenem, pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 9nt0
TitleOXA-23-meropenem, pH 7.5
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE / OXA / antibiotic resistance / inhibitor / meropenem
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
Chem-MER / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSmith, C.A. / Toth, M. / Stewart, N.K. / Vakulenko, S.B.
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: Antimicrob.Agents Chemother. / Year: 2025
Title: Dual mechanism of the OXA-23 carbapenemase inhibition by the carbapenem NA-1-157.
Authors: Toth, M. / Stewart, N.K. / Quan, P. / Khan, M.M.K. / Cox, J. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 15, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)31,5363
Polymers31,0551
Non-polymers4822
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.991, 82.991, 85.128
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-534-

HOH

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Components

#1: Protein Beta-lactamase OXA-23


Mass: 31054.803 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-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
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 EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→37.87 Å / Num. obs: 39875 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 20.7
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1950 / CC1/2: 0.625 / Rpim(I) all: 0.385

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→37.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1949 4.89 %
Rwork0.1672 --
obs0.1689 39822 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 31 135 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142089
X-RAY DIFFRACTIONf_angle_d1.4192840
X-RAY DIFFRACTIONf_dihedral_angle_d19.77811
X-RAY DIFFRACTIONf_chiral_restr0.091318
X-RAY DIFFRACTIONf_plane_restr0.009366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.31791190.27332652X-RAY DIFFRACTION99
1.64-1.680.2388930.23072695X-RAY DIFFRACTION100
1.68-1.730.25851410.20522678X-RAY DIFFRACTION100
1.73-1.790.23551460.18872641X-RAY DIFFRACTION100
1.79-1.850.25551570.19252668X-RAY DIFFRACTION100
1.85-1.930.22331370.19352669X-RAY DIFFRACTION100
1.93-2.020.2061770.16922636X-RAY DIFFRACTION100
2.02-2.120.22771460.16042669X-RAY DIFFRACTION100
2.12-2.260.20011240.16062709X-RAY DIFFRACTION100
2.26-2.430.20931410.16352706X-RAY DIFFRACTION100
2.43-2.670.18371260.16822727X-RAY DIFFRACTION100
2.67-3.060.20691790.16982693X-RAY DIFFRACTION100
3.06-3.850.18511300.15712789X-RAY DIFFRACTION100
3.86-37.870.1841330.15742941X-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)
11.2408-0.4345-1.22720.8739-0.14261.6630.1325-0.11220.20250.2010.18880.06060.12890.23890.00580.2386-0.00650.00080.2423-0.03250.2298-14.9505-21.5987-1.8017
22.3167-0.3235-0.43631.32340.25340.7026-0.01250.287-0.0016-0.0412-0.0114-0.19920.00290.05780.00210.1662-0.02250.0420.24430.04820.19896.8209-27.3648-25.2426
32.49290.1718-0.55411.62780.0512.07470.04790.44160.2042-0.1834-0.0108-0.0148-0.069-0.13230.00130.15740.00780.00760.26380.06810.1833-5.5113-23.6178-26.1285
41.6903-1.2005-0.84070.95670.39162.159-0.0643-0.19740.04110.15390.0558-0.23190.15280.2374-0.00230.18210.0269-0.02790.2290.00580.1499-5.7235-27.5135-9.0921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 208 )
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 273 )

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