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- PDB-9nsy: OXA-23-NA-1-157, 4 minute soak -

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Basic information

Entry
Database: PDB / ID: 9nsy
TitleOXA-23-NA-1-157, 4 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: 1.7 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: To Be Published
Title: Dual Mechanism of the OXA-23 Carbapenemase Inhibition via Catalytic Lysine Decarboxylation and Water Access Restriction by the Carbapenem NA-1-157
Authors: Toth, M. / Stewart, N.K. / 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

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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)31,5523
Polymers31,0551
Non-polymers4982
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.467, 82.467, 84.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
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 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→37.6 Å / Num. obs: 32604 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.095 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1695 / CC1/2: 0.814 / Rpim(I) all: 0.407

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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: 1.7→37.58 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1642 5.06 %
Rwork0.1963 --
obs0.1979 32444 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 5 97 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062082
X-RAY DIFFRACTIONf_angle_d1.1142822
X-RAY DIFFRACTIONf_dihedral_angle_d21.113807
X-RAY DIFFRACTIONf_chiral_restr0.052313
X-RAY DIFFRACTIONf_plane_restr0.005361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.39291330.36082475X-RAY DIFFRACTION98
1.75-1.810.31861310.2992514X-RAY DIFFRACTION99
1.81-1.870.37591540.3012524X-RAY DIFFRACTION99
1.87-1.950.30011440.26112488X-RAY DIFFRACTION99
1.95-2.040.23511770.19572495X-RAY DIFFRACTION100
2.04-2.140.21591200.19082548X-RAY DIFFRACTION100
2.14-2.280.21221290.19212558X-RAY DIFFRACTION99
2.28-2.450.22691690.19032515X-RAY DIFFRACTION100
2.45-2.70.22751210.19582606X-RAY DIFFRACTION100
2.7-3.090.2236830.19382654X-RAY DIFFRACTION100
3.09-3.890.19381390.17622639X-RAY DIFFRACTION100
3.89-37.580.21331420.17552786X-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)
10.14340.0510.13960.12660.13160.1790.3546-0.1090.02390.10610.0114-0.2925-0.37060.09410.03280.3096-0.00060.07720.3413-0.010.278222.3738-14.53449.0336
21.0043-0.28860.0152.7841-0.65650.9571-0.02450.07370.104-0.3220.02830.15650.0382-0.05380.00630.23940.0122-0.06830.1630.01770.211124.4962-1.377619.0096
30.94381.0543-0.27651.3496-0.76822.06480.0278-0.09230.35430.1775-0.0260.0906-0.31510.06990.0010.2574-0.0124-0.00610.1881-0.00460.212626.8708-5.099333.0855
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 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 273 )

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