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- PDB-9nsx: OXA-23-NA-1-157, 3 minute soak -

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Basic information

Entry
Database: PDB / ID: 9nsx
TitleOXA-23-NA-1-157, 3 minute soak
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE / OXA / antibiotic resistance / inhibitor / NA-1-157
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-Y33 / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.57 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)31,6484
Polymers31,0551
Non-polymers5943
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.982, 82.982, 84.976
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-450-

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-Y33 / (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid


Mass: 401.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 47.78 %
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: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.57→37.82 Å / Num. obs: 42061 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 21.4
Reflection shellResolution: 1.57→1.6 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2031 / CC1/2: 0.81 / Rpim(I) all: 0.371

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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: 1.57→37.82 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2065 4.92 %
Rwork0.1801 --
obs0.1814 42003 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 36 140 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062056
X-RAY DIFFRACTIONf_angle_d1.0222786
X-RAY DIFFRACTIONf_dihedral_angle_d21.48786
X-RAY DIFFRACTIONf_chiral_restr0.061309
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.30391290.27082608X-RAY DIFFRACTION99
1.61-1.650.26141350.22362621X-RAY DIFFRACTION100
1.65-1.690.21051350.19092616X-RAY DIFFRACTION100
1.69-1.740.20571320.18682603X-RAY DIFFRACTION100
1.74-1.80.17751300.18442649X-RAY DIFFRACTION100
1.8-1.860.25261320.2072634X-RAY DIFFRACTION100
1.86-1.940.2567960.18972671X-RAY DIFFRACTION100
1.94-2.020.21541390.172652X-RAY DIFFRACTION100
2.02-2.130.18861460.17072630X-RAY DIFFRACTION100
2.13-2.260.17141790.17082606X-RAY DIFFRACTION100
2.26-2.440.22131460.18052657X-RAY DIFFRACTION100
2.44-2.680.19431410.18812676X-RAY DIFFRACTION100
2.68-3.070.25371050.18892727X-RAY DIFFRACTION100
3.07-3.870.19941690.17292703X-RAY DIFFRACTION100
3.87-37.820.19141510.1692885X-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)
10.06590.02570.04480.09080.14330.22270.0186-0.02820.18520.08480.1720.103-0.0319-0.2369-0.00010.3033-0.00460.00910.27780.06790.263614.67922.64636.8197
21.7669-0.05210.75940.7765-0.3750.73250.07640.2103-0.3158-0.01710.00570.06630.04360.0464-0.00230.1386-0.0023-0.00190.2132-0.0640.16996.224523.6244-19.2437
30.76380.04250.19470.78720.03640.48430.0170.16080.08890.10340.00670.1301-0.0009-0.10850.00540.1406-0.0167-0.02280.2631-0.06960.2287-12.05728.2368-23.5259
41.90440.08260.63130.9293-0.05741.56870.03590.4449-0.2043-0.0988-0.0290.0170.04260.031-0.0030.12610.00070.00060.2888-0.090.18625.456623.7235-26.1164
51.5362-1.10420.61780.9841-0.24541.9616-0.017-0.1213-0.0740.15880.00630.216-0.1487-0.25320.00040.16790.00860.01480.2067-0.01390.14555.434927.1724-9.2267
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 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 273 )

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