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- PDB-8rma: Structure of CTX-M-15 complexed with benzoxaborole AK-431 -

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Basic information

Entry
Database: PDB / ID: 8rma
TitleStructure of CTX-M-15 complexed with benzoxaborole AK-431
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: 0.83 Å
AuthorsBeer, M. / Tooke, 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-431
Authors: Beer, M. / Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionJan 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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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)28,9408
Polymers28,2931
Non-polymers6477
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-27 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.700, 45.560, 117.780
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

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1H1U / 2-[(3~{R})-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]ethanoic acid / 4'-methylflavone


Mass: 191.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9BO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8 / 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: 0.66622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.66622 Å / Relative weight: 1
ReflectionResolution: 0.83→39.26 Å / Num. obs: 225963 / % possible obs: 99.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 7.08 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 9.4
Reflection shellResolution: 0.83→0.84 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 11207 / CC1/2: 0.342 / Rpim(I) all: 0.67 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.83→36.03 Å / SU ML: 0.1158 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.6719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1382 11163 4.95 %
Rwork0.1285 214379 -
obs0.129 225542 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.62 Å2
Refinement stepCycle: LAST / Resolution: 0.83→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 36 466 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572231
X-RAY DIFFRACTIONf_angle_d0.97633061
X-RAY DIFFRACTIONf_chiral_restr0.0803346
X-RAY DIFFRACTIONf_plane_restr0.0117415
X-RAY DIFFRACTIONf_dihedral_angle_d11.493860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.83-0.840.39963810.39786854X-RAY DIFFRACTION96.91
0.84-0.850.3883580.36167072X-RAY DIFFRACTION99.21
0.85-0.860.35823990.33277144X-RAY DIFFRACTION99.68
0.86-0.870.31113590.30517030X-RAY DIFFRACTION99.86
0.87-0.880.29283510.27937142X-RAY DIFFRACTION99.84
0.88-0.890.27393480.26097160X-RAY DIFFRACTION99.84
0.89-0.910.26893730.24817077X-RAY DIFFRACTION99.81
0.91-0.920.25743860.2347101X-RAY DIFFRACTION99.8
0.92-0.930.23434010.21397077X-RAY DIFFRACTION99.68
0.93-0.950.22143620.20417162X-RAY DIFFRACTION99.48
0.95-0.970.213690.19567025X-RAY DIFFRACTION99.1
0.97-0.980.20073680.18836990X-RAY DIFFRACTION98.15
0.98-10.18493620.17766835X-RAY DIFFRACTION96.17
1-1.020.17483510.16217175X-RAY DIFFRACTION100
1.02-1.050.17123780.15727167X-RAY DIFFRACTION99.99
1.05-1.070.15133880.14077105X-RAY DIFFRACTION99.99
1.07-1.10.13723570.1187192X-RAY DIFFRACTION99.97
1.1-1.130.11933720.11087166X-RAY DIFFRACTION100
1.13-1.160.10633720.10477152X-RAY DIFFRACTION100
1.16-1.20.11883630.10577192X-RAY DIFFRACTION100
1.2-1.240.10893900.10227175X-RAY DIFFRACTION99.89
1.24-1.290.10993670.10117139X-RAY DIFFRACTION99.55
1.29-1.350.11943510.10247080X-RAY DIFFRACTION98.05
1.35-1.420.11884000.09887190X-RAY DIFFRACTION99.65
1.42-1.510.10313530.0957205X-RAY DIFFRACTION100
1.51-1.620.11233820.09427236X-RAY DIFFRACTION99.93
1.62-1.790.11193430.10067331X-RAY DIFFRACTION100
1.79-2.050.10893850.10317291X-RAY DIFFRACTION99.93
2.05-2.580.11493580.10687309X-RAY DIFFRACTION98.87
2.58-36.030.13234360.13017605X-RAY DIFFRACTION99.99

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