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- PDB-8r30: Structure of CTX-M-15 complexed with benzoxaborole AK-408 -

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Basic information

Entry
Database: PDB / ID: 8r30
TitleStructure of CTX-M-15 complexed with benzoxaborole AK-408
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Inhibitor / beta-lactamase / SBL / antibiotic resistance / boronate
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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: 0.85 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-408
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)29,32213
Polymers28,2931
Non-polymers1,02912
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-57 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.252, 45.506, 117.416
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, 334 molecules

#2: Chemical ChemComp-XR3 / N-[[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]methyl]-4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]benzenesulfonamide


Mass: 348.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13BN2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 0.85→42.43 Å / Num. obs: 208397 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 7.57 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Net I/σ(I): 11.7
Reflection shellResolution: 0.85→0.86 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 10188 / CC1/2: 0.334 / Rpim(I) all: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.85→31.72 Å / SU ML: 0.1016 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.0195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1368 10441 5.01 %
Rwork0.1243 197786 -
obs0.125 208227 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.47 Å2
Refinement stepCycle: LAST / Resolution: 0.85→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 57 322 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552220
X-RAY DIFFRACTIONf_angle_d0.96473041
X-RAY DIFFRACTIONf_chiral_restr0.0799342
X-RAY DIFFRACTIONf_plane_restr0.0126409
X-RAY DIFFRACTIONf_dihedral_angle_d11.4805852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.860.3583260.33666524X-RAY DIFFRACTION99.94
0.86-0.870.33543580.32236537X-RAY DIFFRACTION99.83
0.87-0.880.30013330.30296479X-RAY DIFFRACTION99.87
0.88-0.890.33013190.29166580X-RAY DIFFRACTION99.86
0.89-0.90.26383630.28156488X-RAY DIFFRACTION99.9
0.9-0.920.26963390.26326513X-RAY DIFFRACTION100
0.92-0.930.27573290.23846589X-RAY DIFFRACTION99.97
0.93-0.940.21373470.22356520X-RAY DIFFRACTION99.99
0.94-0.960.2093510.21056538X-RAY DIFFRACTION99.96
0.96-0.970.20113650.19956505X-RAY DIFFRACTION99.99
0.97-0.990.20663730.18446525X-RAY DIFFRACTION99.87
0.99-1.010.18513470.17116581X-RAY DIFFRACTION100
1.01-1.030.18313830.15376482X-RAY DIFFRACTION100
1.03-1.050.15463590.14776554X-RAY DIFFRACTION99.99
1.05-1.070.14543300.13096554X-RAY DIFFRACTION100
1.07-1.10.12573540.11176582X-RAY DIFFRACTION99.99
1.1-1.120.12043480.10246561X-RAY DIFFRACTION99.96
1.12-1.150.10913420.09856564X-RAY DIFFRACTION100
1.15-1.190.10633240.09516606X-RAY DIFFRACTION100
1.19-1.230.11113430.09096603X-RAY DIFFRACTION100
1.23-1.270.1033410.08816626X-RAY DIFFRACTION100
1.27-1.320.09813190.08846584X-RAY DIFFRACTION99.94
1.32-1.380.09813670.09116628X-RAY DIFFRACTION99.93
1.38-1.450.1013140.08716620X-RAY DIFFRACTION100
1.45-1.540.10243440.08366643X-RAY DIFFRACTION99.99
1.54-1.660.09593380.08786652X-RAY DIFFRACTION100
1.66-1.830.10333730.09686672X-RAY DIFFRACTION100
1.83-2.10.11093690.10046689X-RAY DIFFRACTION100
2.1-2.640.12573270.116792X-RAY DIFFRACTION99.87
2.64-31.720.15154160.14156995X-RAY DIFFRACTION99.97

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