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- PDB-8cum: X-ray crystal structure of OXA-24/40 in complex with sulfonamidob... -

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Basic information

Entry
Database: PDB / ID: 8cum
TitleX-ray crystal structure of OXA-24/40 in complex with sulfonamidoboronic acid 6d
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / Carbapenemase / Inhibitor / BATSI / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / beta-lactamase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / Chem-OZ0 / Beta-lactamase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsFernando, M.C. / Wallar, B.J. / Powers, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: Antibiotics / Year: 2023
Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat ...Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii .
Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / ...Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / Hujer, A.M. / Prati, F. / Powers, R.A. / Bonomo, R.A. / Caselli, E.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5958
Polymers27,7181
Non-polymers8787
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Monomeric biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.190, 102.190, 85.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-626-

HOH

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Components

#1: Protein Beta-lactamase / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 ...Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / OXA24 B-lactamase / Oxa40


Mass: 27717.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-OZ0 / 3-({[(1S)-1-boronopropyl]sulfamoyl}methyl)benzoic acid


Mass: 301.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16BNO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5 2% PEG 400 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.49→55.26 Å / Num. obs: 74330 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 19.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.035 / Rrim(I) all: 0.099 / Net I/σ(I): 12.6 / Num. measured all: 597202
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.49-1.537.92.2514230653890.4190.8462.4070.999.2
6.66-55.266.80.02965059620.9990.0110.0314199.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 1.49→51.09 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 3689 4.97 %
Rwork0.1893 70570 -
obs0.1903 74259 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 25.99 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 1.49→51.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 64 287 2278
Biso mean--32.74 37.18 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.510.43111370.40852640277798
1.51-1.530.43171300.37462682281299
1.53-1.550.36491410.358726722813100
1.55-1.580.31171210.31612690281199
1.58-1.60.30691520.309326562808100
1.6-1.630.29991440.276526712815100
1.63-1.650.30861130.270626962809100
1.65-1.680.27041470.25826732820100
1.68-1.720.24811470.246326662813100
1.72-1.750.22671390.242427062845100
1.75-1.790.25391380.227126862824100
1.79-1.830.28031380.235426922830100
1.83-1.880.27311520.216326942846100
1.88-1.930.22421370.199127082845100
1.93-1.980.19731430.190526822825100
1.98-2.050.20991450.183327222867100
2.05-2.120.21591390.173227072846100
2.12-2.210.18931360.17826982834100
2.21-2.310.21371340.179727462880100
2.31-2.430.18251530.174927152868100
2.43-2.580.20291350.178727382873100
2.58-2.780.20751720.181627292901100
2.78-3.060.20751320.181127612893100
3.06-3.50.17051530.160127852938100
3.5-4.410.1521570.138727882945100
4.41-51.090.19961540.183329673121100

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