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- PDB-8rwp: KPC-2 G89D Mutant in Complex with Avibactam -

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Basic information

Entry
Database: PDB / ID: 8rwp
TitleKPC-2 G89D Mutant in Complex with Avibactam
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / Beta-Lactamase / Inhibitor / Antibiotic Resistance
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
: / Chem-NXL / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsBeer, M. / Hinchliffe, P. / Tooke, C.L. / Spencer, J.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/10 United Kingdom
European Research Council (ERC)101021207European Union
CitationJournal: Chem Sci / Year: 2024
Title: Dynamical responses predict a distal site that modulates activity in an antibiotic resistance enzyme.
Authors: Beer, M. / Oliveira, A.S.F. / Tooke, C.L. / Hinchliffe, P. / Tsz Yan Li, A. / Balega, B. / Spencer, J. / Mulholland, A.J.
History
DepositionFeb 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 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)31,5856
Polymers30,8651
Non-polymers7215
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-30 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.140, 78.490, 55.640
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-698-

HOH

21A-889-

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: 30864.666 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) / References: UniProt: Q9F663, beta-lactamase

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Non-polymers , 5 types, 365 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-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#4: Chemical ChemComp-A1H3M / (2~{S})-5-azanylidene-1-methanoyl-piperidine-2-carboxamide / Avibactam


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 42.18 %
Crystal growTemperature: 293.15 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: 0.8153 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8153 Å / Relative weight: 1
ReflectionResolution: 1.19→45.39 Å / Num. obs: 84567 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 1 / Rpim(I) all: 0.033 / Net I/σ(I): 10
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 8048 / CC1/2: 0.295 / Rpim(I) all: 1.005 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→45.39 Å / SU ML: 0.1835 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1794 4145 4.9 %
Rwork0.1554 80422 -
obs0.1566 84567 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.41 Å2
Refinement stepCycle: LAST / Resolution: 1.19→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 45 360 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812247
X-RAY DIFFRACTIONf_angle_d0.99883078
X-RAY DIFFRACTIONf_chiral_restr0.0724338
X-RAY DIFFRACTIONf_plane_restr0.0124405
X-RAY DIFFRACTIONf_dihedral_angle_d12.2906824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20.45491290.4622562X-RAY DIFFRACTION95.9
1.2-1.220.45161260.45552511X-RAY DIFFRACTION95.1
1.22-1.230.44541350.4282585X-RAY DIFFRACTION97.14
1.23-1.250.40721650.40632600X-RAY DIFFRACTION99.03
1.25-1.260.38381470.37672643X-RAY DIFFRACTION99.61
1.26-1.280.40811340.35932656X-RAY DIFFRACTION99.57
1.28-1.30.3591530.35012671X-RAY DIFFRACTION99.96
1.3-1.320.34381170.32712675X-RAY DIFFRACTION99.79
1.32-1.340.29781320.31182635X-RAY DIFFRACTION99.78
1.34-1.360.33671340.29392679X-RAY DIFFRACTION99.68
1.36-1.390.28161310.28022666X-RAY DIFFRACTION99.89
1.39-1.410.2691260.24592675X-RAY DIFFRACTION99.79
1.41-1.440.25031430.22322688X-RAY DIFFRACTION99.82
1.44-1.470.2541400.19722659X-RAY DIFFRACTION100
1.47-1.50.22271430.19322675X-RAY DIFFRACTION100
1.5-1.530.22171280.1672679X-RAY DIFFRACTION99.96
1.53-1.570.22721380.15622701X-RAY DIFFRACTION99.93
1.57-1.620.18971560.14672632X-RAY DIFFRACTION99.79
1.62-1.660.19281320.13982690X-RAY DIFFRACTION99.89
1.66-1.720.171330.13422708X-RAY DIFFRACTION99.93
1.72-1.780.17641310.12692709X-RAY DIFFRACTION100
1.78-1.850.15921370.11852677X-RAY DIFFRACTION100
1.85-1.930.1891670.11792679X-RAY DIFFRACTION99.89
1.93-2.030.13581450.10182699X-RAY DIFFRACTION99.96
2.03-2.160.13921410.11082718X-RAY DIFFRACTION99.97
2.16-2.330.15141340.11532732X-RAY DIFFRACTION100
2.33-2.560.13171510.11182731X-RAY DIFFRACTION100
2.56-2.930.12361120.12282784X-RAY DIFFRACTION99.97
2.93-3.70.15061430.13632779X-RAY DIFFRACTION99.93
3.7-45.390.1581420.15312924X-RAY DIFFRACTION99.93

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