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- PDB-9f0v: Structure of KPC-2 complexed with benzoxaborole AK-63 -

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Basic information

Entry
Database: PDB / ID: 9f0v
TitleStructure of KPC-2 complexed with benzoxaborole AK-63
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: 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 KPC-2 complexed with benzoxaborole AK-63
Authors: Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionApr 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 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)31,4698
Polymers30,8071
Non-polymers6627
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-55 kcal/mol
Surface area11170 Å2
Unit cell
Length a, b, c (Å)60.150, 79.080, 55.850
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-513-

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, 416 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1H8R / [(3~{S})-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]methanamine


Mass: 162.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BNO2 / 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.: 409 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
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: 0.7745 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7745 Å / Relative weight: 1
ReflectionResolution: 1.1→36.32 Å / Num. obs: 108335 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 13.41 Å2 / CC1/2: 1 / Rpim(I) all: 0.963 / Net I/σ(I): 9.8
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5355 / CC1/2: 0.337 / Rpim(I) all: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→32.27 Å / SU ML: 0.1443 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.1477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1674 5629 5.2 %
Rwork0.1396 102706 -
obs0.1411 108335 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.1→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 39 409 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042314
X-RAY DIFFRACTIONf_angle_d1.14233183
X-RAY DIFFRACTIONf_chiral_restr0.0743351
X-RAY DIFFRACTIONf_plane_restr0.012426
X-RAY DIFFRACTIONf_dihedral_angle_d11.7214851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.40371710.38993298X-RAY DIFFRACTION96.09
1.11-1.130.35091900.34583340X-RAY DIFFRACTION99.55
1.13-1.140.33371890.32583413X-RAY DIFFRACTION99.75
1.14-1.150.32211980.31193345X-RAY DIFFRACTION99.89
1.15-1.170.30861810.30043373X-RAY DIFFRACTION99.89
1.17-1.180.32641620.28983415X-RAY DIFFRACTION99.8
1.18-1.20.29121990.27933388X-RAY DIFFRACTION99.97
1.2-1.220.26422040.2733382X-RAY DIFFRACTION99.94
1.22-1.240.25261990.26363384X-RAY DIFFRACTION99.97
1.24-1.260.27611800.24783390X-RAY DIFFRACTION99.94
1.26-1.280.31590.2353447X-RAY DIFFRACTION99.97
1.28-1.30.23521970.22113376X-RAY DIFFRACTION99.92
1.3-1.330.27441960.20983402X-RAY DIFFRACTION99.92
1.33-1.360.23761530.19163409X-RAY DIFFRACTION99.89
1.36-1.390.22721780.18993431X-RAY DIFFRACTION99.92
1.39-1.420.21171730.16783401X-RAY DIFFRACTION99.97
1.42-1.450.21971710.15593439X-RAY DIFFRACTION100
1.45-1.490.20471930.14073426X-RAY DIFFRACTION100
1.49-1.540.17722270.13153382X-RAY DIFFRACTION100
1.54-1.590.17581820.12113449X-RAY DIFFRACTION99.92
1.59-1.640.13661800.10783419X-RAY DIFFRACTION99.94
1.64-1.710.15771820.10413421X-RAY DIFFRACTION99.97
1.71-1.790.12251850.10553446X-RAY DIFFRACTION100
1.79-1.880.11861720.1063466X-RAY DIFFRACTION99.97
1.88-20.13621710.10743476X-RAY DIFFRACTION99.97
2-2.150.13462090.1053454X-RAY DIFFRACTION99.97
2.15-2.370.1252080.10343438X-RAY DIFFRACTION100
2.37-2.710.12862090.10663487X-RAY DIFFRACTION99.97
2.71-3.420.1431830.11523546X-RAY DIFFRACTION100
3.42-32.270.15822280.13123663X-RAY DIFFRACTION99.95

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