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- PDB-8rws: KPC-2 G89D/E166Q Mutant in Complex with Meropenem -

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Basic information

Entry
Database: PDB / ID: 8rws
TitleKPC-2 G89D/E166Q Mutant in Complex with Meropenem
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / Beta-Lactamase / Carbapenem / 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-MER / Chem-O2F / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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)31,9236
Polymers30,8641
Non-polymers1,0595
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-22 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.117, 78.753, 56.155
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

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-O2F / (2S,3R,4R)-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.88 %
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: 1.09→36.39 Å / Num. obs: 110930 / % possible obs: 99.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 13.45 Å2 / Rpim(I) all: 0.042 / Net I/σ(I): 7
Reflection shellResolution: 1.09→1.11 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5376 / CC1/2: 0.324 / Rpim(I) all: 1.105

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→36.39 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 5441 4.93 %
Rwork0.174 104868 -
obs0.1753 110309 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.28 Å2
Refinement stepCycle: LAST / Resolution: 1.09→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 67 291 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712333
X-RAY DIFFRACTIONf_angle_d1.01883215
X-RAY DIFFRACTIONf_chiral_restr0.075351
X-RAY DIFFRACTIONf_plane_restr0.013426
X-RAY DIFFRACTIONf_dihedral_angle_d13.367868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.49581600.46923049X-RAY DIFFRACTION86.94
1.1-1.120.43461520.45693340X-RAY DIFFRACTION95.46
1.12-1.130.44361760.44143420X-RAY DIFFRACTION97.72
1.13-1.140.4342090.42453431X-RAY DIFFRACTION98.38
1.14-1.160.43581810.40133423X-RAY DIFFRACTION98.15
1.16-1.170.38361790.38513474X-RAY DIFFRACTION98.84
1.17-1.190.3931880.37433448X-RAY DIFFRACTION99.02
1.19-1.210.35611970.35543455X-RAY DIFFRACTION98.54
1.21-1.230.31521760.33543452X-RAY DIFFRACTION98.59
1.23-1.250.37852080.32573462X-RAY DIFFRACTION99.35
1.25-1.270.3151700.30913465X-RAY DIFFRACTION99.21
1.27-1.290.29171590.28113477X-RAY DIFFRACTION98.97
1.29-1.320.3121730.26843495X-RAY DIFFRACTION99.14
1.32-1.340.2821600.25113518X-RAY DIFFRACTION99.19
1.34-1.370.24621660.23943514X-RAY DIFFRACTION99.27
1.37-1.410.25941760.22643500X-RAY DIFFRACTION99.49
1.41-1.440.24761610.19453538X-RAY DIFFRACTION99.6
1.44-1.480.21181980.18173499X-RAY DIFFRACTION99.65
1.48-1.520.18381810.16343500X-RAY DIFFRACTION99.68
1.52-1.570.19762070.1543502X-RAY DIFFRACTION99.81
1.57-1.630.18512170.14353491X-RAY DIFFRACTION99.76
1.63-1.690.18261610.13843534X-RAY DIFFRACTION99.86
1.69-1.770.20281850.1433555X-RAY DIFFRACTION99.92
1.77-1.860.18411830.13573555X-RAY DIFFRACTION99.97
1.86-1.980.17461910.12493538X-RAY DIFFRACTION100
1.98-2.130.1442000.1223562X-RAY DIFFRACTION99.89
2.13-2.350.14531980.11883564X-RAY DIFFRACTION99.81
2.35-2.690.13851680.12333625X-RAY DIFFRACTION99.97
2.69-3.390.15781760.13753657X-RAY DIFFRACTION100
3.39-36.390.17171850.15123825X-RAY DIFFRACTION99.95

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