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- PDB-9fbt: Structure of KPC-2 complexed with benzoxaborole AK-431 -

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Basic information

Entry
Database: PDB / ID: 9fbt
TitleStructure of KPC-2 complexed with benzoxaborole AK-431
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 / beta-lactamase activity / 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: 1.07 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 KPC-2 complexed with benzoxaborole AK-431
Authors: Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 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)31,99712
Polymers30,8071
Non-polymers1,19111
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-76 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.973, 78.550, 55.885
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-308-

SO4

21A-502-

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) / Strain (production host): Solu / References: UniProt: Q9F663, beta-lactamase

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Non-polymers , 6 types, 384 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.: 7 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-A1IB7 / [2-[(1~{S})-1,3-bis(oxidanyl)-3-oxidanylidene-propyl]phenyl]-bis(oxidanyl)-$l^{4}-borane


Mass: 211.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12BO5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 292 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: 0.7446 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7446 Å / Relative weight: 1
ReflectionResolution: 1.07→47.67 Å / Num. obs: 116684 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 11.13 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.064 / Net I/σ(I): 5.9
Reflection shellResolution: 1.07→1.09 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 71379 / CC1/2: 0.327 / Rpim(I) all: 1.034 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.07→47.67 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 1962 1.69 %
Rwork0.1614 114011 -
obs0.1618 115973 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.53 Å2
Refinement stepCycle: LAST / Resolution: 1.07→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 71 373 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762337
X-RAY DIFFRACTIONf_angle_d1.03083218
X-RAY DIFFRACTIONf_chiral_restr0.0781347
X-RAY DIFFRACTIONf_plane_restr0.0074432
X-RAY DIFFRACTIONf_dihedral_angle_d11.7501860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.10.40031310.38837473X-RAY DIFFRACTION92.32
1.1-1.130.3591350.35318010X-RAY DIFFRACTION99.15
1.13-1.160.32761220.31938151X-RAY DIFFRACTION99.95
1.16-1.20.30361400.2948089X-RAY DIFFRACTION99.96
1.2-1.240.32711370.27688144X-RAY DIFFRACTION99.96
1.24-1.290.27121330.25588128X-RAY DIFFRACTION99.94
1.29-1.350.27681660.238093X-RAY DIFFRACTION99.93
1.35-1.420.22691430.19768172X-RAY DIFFRACTION99.92
1.42-1.510.19251760.16548139X-RAY DIFFRACTION99.94
1.51-1.620.17181390.13478184X-RAY DIFFRACTION99.98
1.62-1.790.16931220.11918227X-RAY DIFFRACTION99.96
1.79-2.050.16461360.10848269X-RAY DIFFRACTION99.96
2.05-2.580.13161290.11398322X-RAY DIFFRACTION99.99
2.58-47.670.14031530.12898610X-RAY DIFFRACTION99.93

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