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- PDB-8r2y: Structure of CTX-M-15 complexed with benzoxaborole AK-29 -

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Basic information

Entry
Database: PDB / ID: 8r2y
TitleStructure of CTX-M-15 complexed with benzoxaborole AK-29
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Inhibitor / beta-lactamase / SBL / antibiotic resistance
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
2,1-benzoxaborol-1(3H)-ol / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 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-29
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)29,35615
Polymers28,2931
Non-polymers1,06314
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-77 kcal/mol
Surface area11090 Å2
Unit cell
Length a, b, c (Å)44.430, 45.850, 116.880
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 , 7 types, 346 molecules

#2: Chemical ChemComp-6M9 / 2,1-benzoxaborol-1(3H)-ol


Mass: 133.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / 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: 1.03→35.37 Å / Num. obs: 118620 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 11.65 Å2 / CC1/2: 1 / Rpim(I) all: 0.034 / Net I/σ(I): 9.8
Reflection shellResolution: 1.03→1.05 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5861 / CC1/2: 0.27 / Rpim(I) all: 0.912

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.03→28 Å / SU ML: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.8694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1543 5743 4.86 %
Rwork0.1344 112465 -
obs0.1354 118208 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.68 Å2
Refinement stepCycle: LAST / Resolution: 1.03→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 58 332 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632223
X-RAY DIFFRACTIONf_angle_d0.95123044
X-RAY DIFFRACTIONf_chiral_restr0.0778339
X-RAY DIFFRACTIONf_plane_restr0.0117408
X-RAY DIFFRACTIONf_dihedral_angle_d11.5313848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.38631850.35833537X-RAY DIFFRACTION95.05
1.04-1.050.35061860.33693631X-RAY DIFFRACTION98.07
1.05-1.070.31711920.31183702X-RAY DIFFRACTION99.67
1.07-1.080.33172000.30283709X-RAY DIFFRACTION99.95
1.08-1.090.30371850.27423721X-RAY DIFFRACTION99.95
1.09-1.110.27792160.26573711X-RAY DIFFRACTION99.87
1.11-1.130.26191720.24153700X-RAY DIFFRACTION99.9
1.13-1.140.25191980.2353734X-RAY DIFFRACTION99.95
1.14-1.160.23011960.22213722X-RAY DIFFRACTION99.97
1.16-1.180.21321820.20623740X-RAY DIFFRACTION99.95
1.18-1.20.21762010.1983720X-RAY DIFFRACTION100
1.2-1.220.19621840.19183726X-RAY DIFFRACTION99.95
1.22-1.240.21211900.18263735X-RAY DIFFRACTION99.8
1.24-1.270.19821790.16953749X-RAY DIFFRACTION99.75
1.27-1.30.19592060.16173686X-RAY DIFFRACTION99.57
1.3-1.330.18741890.15543725X-RAY DIFFRACTION99.24
1.33-1.360.18792050.15393688X-RAY DIFFRACTION98.63
1.36-1.40.14671950.1343731X-RAY DIFFRACTION99.59
1.4-1.440.15392200.12173709X-RAY DIFFRACTION99.97
1.44-1.490.13521580.10983809X-RAY DIFFRACTION100
1.49-1.540.11451770.10263758X-RAY DIFFRACTION100
1.54-1.60.13221790.09993782X-RAY DIFFRACTION99.97
1.6-1.670.11681890.09743769X-RAY DIFFRACTION99.97
1.67-1.760.13422010.09833787X-RAY DIFFRACTION100
1.76-1.870.13031810.10073786X-RAY DIFFRACTION100
1.87-2.020.11891880.09913820X-RAY DIFFRACTION99.9
2.02-2.220.11641970.09923827X-RAY DIFFRACTION99.95
2.22-2.540.11761980.10243804X-RAY DIFFRACTION99.55
2.54-3.20.13641880.11733897X-RAY DIFFRACTION99.93
3.2-280.14972060.13794050X-RAY DIFFRACTION99.95

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