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- PDB-8cul: Xray ray crystal structure of OXA-24/40 in complex with CR167 -

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Basic information

Entry
Database: PDB / ID: 8cul
TitleXray ray crystal structure of OXA-24/40 in complex with CR167
ComponentsBeta-lactamase
KeywordsHydrolase/Inhibitor / carbapenemase / BATSI / inhibitor / HYDROLASE / Hydrolase-Inhibitor complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase
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-0N3 / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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)27,9912
Polymers27,7181
Non-polymers2731
Water2,216123
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)102.585, 102.585, 86.174
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-512-

HOH

21A-523-

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-0N3 / 3-({[(dihydroxyboranyl)methyl]sulfamoyl}methyl)benzoic acid


Mass: 273.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12BNO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium, pH 7.5, 2% v/v 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-D / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.01→72.54 Å / Num. obs: 26105 / % possible obs: 93.8 % / Redundancy: 7.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.073 / Rrim(I) all: 0.198 / Net I/σ(I): 7.6
Reflection shell

Num. unique obs: 1305 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.015-2.1196.61.2485900.60.5211.3471.666.8
6.007-72.5397.10.06892190.9970.0260.0732099.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 2.01→72.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.768 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1280 4.9 %RANDOM
Rwork0.212 ---
obs0.2141 24837 84.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.99 Å2 / Biso mean: 39.43 Å2 / Biso min: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 2.01→72.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 18 123 2047
Biso mean--40.46 46.4 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121982
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.652686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88823.76393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.883158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021490
LS refinement shellResolution: 2.013→2.065 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 22 -
Rwork0.271 471 -
all-493 -
obs--21.9 %

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