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- PDB-8rwr: KPC-2 G89D/E166Q Mutant in Complex with Imipenem -

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Basic information

Entry
Database: PDB / ID: 8rwr
TitleKPC-2 G89D/E166Q Mutant in Complex with Imipenem
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 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 / MOLECULAR REPLACEMENT / Resolution: 1.03 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)31,7516
Polymers30,8641
Non-polymers8875
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-16 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.213, 79.455, 55.679
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

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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: 30863.682 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, 286 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1H3N / (2~{R},4~{R})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1H3O / (2~{R},4~{S})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / d1_2S_imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2 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: 0.81531 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81531 Å / Relative weight: 1
ReflectionResolution: 1.03→39.73 Å / Num. obs: 130263 / % possible obs: 98.5 % / Redundancy: 13.6 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 1 / Rpim(I) all: 0.031 / Net I/σ(I): 9.6
Reflection shellResolution: 1.03→1.05 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6249 / CC1/2: 0.347 / Rpim(I) all: 1.104

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→39.73 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1744 6324 4.87 %
Rwork0.1585 123604 -
obs0.1592 129928 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.62 Å2
Refinement stepCycle: LAST / Resolution: 1.03→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 56 281 2347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712305
X-RAY DIFFRACTIONf_angle_d1.17783160
X-RAY DIFFRACTIONf_chiral_restr0.0751347
X-RAY DIFFRACTIONf_plane_restr0.0136421
X-RAY DIFFRACTIONf_dihedral_angle_d13.4163856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.46611760.44113816X-RAY DIFFRACTION92.77
1.04-1.050.45822050.4263982X-RAY DIFFRACTION95.59
1.05-1.070.42972250.4163989X-RAY DIFFRACTION96.54
1.07-1.080.39741890.39824018X-RAY DIFFRACTION96.82
1.08-1.090.37242140.37834048X-RAY DIFFRACTION97.19
1.09-1.110.33912130.35064034X-RAY DIFFRACTION97.36
1.11-1.130.32821850.34344048X-RAY DIFFRACTION97.4
1.13-1.140.35911930.32714072X-RAY DIFFRACTION97.55
1.14-1.160.26432000.28884082X-RAY DIFFRACTION97.65
1.16-1.180.30892230.28144041X-RAY DIFFRACTION97.73
1.18-1.20.3071890.27034085X-RAY DIFFRACTION97.92
1.2-1.220.25962090.25654060X-RAY DIFFRACTION97.98
1.22-1.240.23512080.24334121X-RAY DIFFRACTION98.21
1.24-1.270.23542110.2294061X-RAY DIFFRACTION98.27
1.27-1.30.21452010.21724141X-RAY DIFFRACTION98.32
1.3-1.330.23362010.19574125X-RAY DIFFRACTION98.52
1.33-1.360.18442180.18074100X-RAY DIFFRACTION98.67
1.36-1.40.18282250.16314104X-RAY DIFFRACTION98.75
1.4-1.440.16832020.15044147X-RAY DIFFRACTION98.98
1.44-1.490.17382220.13824137X-RAY DIFFRACTION99.18
1.49-1.540.14951760.13124190X-RAY DIFFRACTION99.05
1.54-1.60.15742230.1234155X-RAY DIFFRACTION99.27
1.6-1.670.14372490.11484158X-RAY DIFFRACTION99.41
1.67-1.760.14242230.11654162X-RAY DIFFRACTION99.57
1.76-1.870.13022290.11574209X-RAY DIFFRACTION99.64
1.87-2.020.12922510.10844162X-RAY DIFFRACTION99.77
2.02-2.220.13512150.10894268X-RAY DIFFRACTION99.84
2.22-2.540.12722300.11284254X-RAY DIFFRACTION99.98
2.54-3.20.12212190.12834306X-RAY DIFFRACTION100
3.2-39.730.17792000.15074529X-RAY DIFFRACTION99.94

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