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- PDB-8r2z: Structure of CTX-M-15 complexed with benzoxaborole AK-425 -

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Basic information

Entry
Database: PDB / ID: 8r2z
TitleStructure of CTX-M-15 complexed with benzoxaborole AK-425
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Inhibitor / beta-lactamase / SBL / antibiotic resistance / boronate
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T016035/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of CTX-M-15 complexed with benzoxaborole AK-425
Authors: Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,99610
Polymers28,2931
Non-polymers7039
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-48 kcal/mol
Surface area10970 Å2
Unit cell
Length a, b, c (Å)44.438, 45.514, 116.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: G3G192, beta-lactamase

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Non-polymers , 6 types, 274 molecules

#2: Chemical ChemComp-XR9 / (9S)-7-oxidanyl-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-triene-9-carbonitrile


Mass: 158.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6BNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.6741 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6741 Å / Relative weight: 1
ReflectionResolution: 1.098→58.461 Å / Num. obs: 97267 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 11.67 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 7.7
Reflection shellResolution: 1.098→1.117 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4763 / CC1/2: 0.337 / Rpim(I) all: 1.162 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
autoPROCdata scaling
autoPROCdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→41.54 Å / SU ML: 0.1214 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.0502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1677 4807 4.95 %
Rwork0.1398 92245 -
obs0.1412 97052 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.67 Å2
Refinement stepCycle: LAST / Resolution: 1.1→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 39 265 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672212
X-RAY DIFFRACTIONf_angle_d1.00033034
X-RAY DIFFRACTIONf_chiral_restr0.078340
X-RAY DIFFRACTIONf_plane_restr0.0109410
X-RAY DIFFRACTIONf_dihedral_angle_d11.6839848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.35281450.31382944X-RAY DIFFRACTION95.84
1.11-1.120.31171420.28672965X-RAY DIFFRACTION98.07
1.12-1.140.28721710.28423080X-RAY DIFFRACTION98.84
1.14-1.150.30871500.27172973X-RAY DIFFRACTION99.24
1.15-1.170.27841750.25483047X-RAY DIFFRACTION99.75
1.17-1.180.28991470.24513015X-RAY DIFFRACTION99.15
1.18-1.20.2481600.23833083X-RAY DIFFRACTION99.63
1.2-1.220.21921710.22073002X-RAY DIFFRACTION99.62
1.22-1.240.24491550.21213052X-RAY DIFFRACTION99.47
1.24-1.260.22941750.21263019X-RAY DIFFRACTION99.97
1.26-1.280.26231470.20533084X-RAY DIFFRACTION99.6
1.28-1.30.23151230.19243129X-RAY DIFFRACTION99.91
1.3-1.330.22551460.17763019X-RAY DIFFRACTION99.75
1.33-1.350.18581640.17913036X-RAY DIFFRACTION98.52
1.35-1.380.21261710.16653069X-RAY DIFFRACTION99.97
1.38-1.420.1611610.14183054X-RAY DIFFRACTION99.91
1.42-1.450.18311470.12483069X-RAY DIFFRACTION99.97
1.45-1.490.15681650.12483087X-RAY DIFFRACTION99.97
1.49-1.530.15221610.11523075X-RAY DIFFRACTION100
1.53-1.580.1531520.11683111X-RAY DIFFRACTION100
1.58-1.640.14421800.11193046X-RAY DIFFRACTION100
1.64-1.710.1381440.10843097X-RAY DIFFRACTION100
1.71-1.780.14521810.10573092X-RAY DIFFRACTION100
1.78-1.880.14331590.10593105X-RAY DIFFRACTION100
1.88-20.13071630.10783112X-RAY DIFFRACTION100
2-2.150.12861360.10283146X-RAY DIFFRACTION100
2.15-2.370.12971820.10743133X-RAY DIFFRACTION100
2.37-2.710.14341730.10933074X-RAY DIFFRACTION98.36
2.71-3.410.14321810.12373184X-RAY DIFFRACTION99.91
3.41-41.540.17941800.15093343X-RAY DIFFRACTION99.97

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