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- PDB-9f0t: Structure of KPC-2 complexed with benzoxaborole AK-110 -

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Basic information

Entry
Database: PDB / ID: 9f0t
TitleStructure of KPC-2 complexed with benzoxaborole AK-110
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
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
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.98 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 KPC-2 complexed with benzoxaborole AK-110
Authors: Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionApr 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,88611
Polymers30,8071
Non-polymers1,08010
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-71 kcal/mol
Surface area11410 Å2
Unit cell
Length a, b, c (Å)59.877, 78.323, 55.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-309-

SO4

21A-485-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 30806.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: Q9F663, beta-lactamase

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Non-polymers , 5 types, 397 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1H8S / ~{N}-[[(3~{S})-1-oxidanyl-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]pyrrolidine-1-sulfonamide


Mass: 296.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17BN2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 5% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.81 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 0.98→55.98 Å / Num. obs: 151124 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 11.33 Å2 / CC1/2: 1 / Rpim(I) all: 0.039 / Net I/σ(I): 9.2
Reflection shellResolution: 0.98→1 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 7422 / CC1/2: 0.322 / Rpim(I) all: 1.154 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.98→47.57 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1618 7464 5.04 %
Rwork0.1418 140598 -
obs0.1428 148062 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.51 Å2
Refinement stepCycle: LAST / Resolution: 0.98→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 63 387 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662405
X-RAY DIFFRACTIONf_angle_d1.05933313
X-RAY DIFFRACTIONf_chiral_restr0.0742361
X-RAY DIFFRACTIONf_plane_restr0.0138443
X-RAY DIFFRACTIONf_dihedral_angle_d12.0326890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.46931450.472886X-RAY DIFFRACTION61.06
0.99-10.49482150.45893960X-RAY DIFFRACTION83.17
1-1.020.42292450.43334612X-RAY DIFFRACTION97.37
1.02-1.030.392530.41614669X-RAY DIFFRACTION99.72
1.03-1.040.38642440.38524756X-RAY DIFFRACTION99.88
1.04-1.060.36592400.36444738X-RAY DIFFRACTION99.94
1.06-1.070.342610.33324722X-RAY DIFFRACTION99.9
1.07-1.090.30722320.30494735X-RAY DIFFRACTION99.94
1.09-1.10.28652650.27934752X-RAY DIFFRACTION99.86
1.1-1.120.26482660.25044752X-RAY DIFFRACTION99.96
1.12-1.140.23222400.22314715X-RAY DIFFRACTION99.92
1.14-1.160.22682490.20544742X-RAY DIFFRACTION99.94
1.16-1.180.21882380.19534743X-RAY DIFFRACTION99.9
1.18-1.210.20612390.184776X-RAY DIFFRACTION99.98
1.21-1.230.19472510.1714765X-RAY DIFFRACTION99.92
1.23-1.260.19362700.16314741X-RAY DIFFRACTION99.94
1.26-1.30.1762450.15184749X-RAY DIFFRACTION99.98
1.3-1.330.16962560.13914771X-RAY DIFFRACTION99.92
1.33-1.370.15682560.12884776X-RAY DIFFRACTION99.94
1.37-1.410.14232530.11994765X-RAY DIFFRACTION99.96
1.41-1.460.13512530.11264775X-RAY DIFFRACTION99.96
1.46-1.520.13242770.10474756X-RAY DIFFRACTION99.98
1.52-1.590.13372850.10354751X-RAY DIFFRACTION99.94
1.59-1.680.11432620.09564792X-RAY DIFFRACTION99.98
1.68-1.780.11752510.14822X-RAY DIFFRACTION100
1.78-1.920.12382850.10364792X-RAY DIFFRACTION100
1.92-2.110.12262420.10294844X-RAY DIFFRACTION99.96
2.11-2.420.11722300.10534907X-RAY DIFFRACTION100
2.42-3.040.12922560.11094915X-RAY DIFFRACTION100
3.05-47.570.15972600.13385119X-RAY DIFFRACTION99.89

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