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- PDB-8rwq: KPC-2 G89D/E166Q Mutant Apo Structure -

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Basic information

Entry
Database: PDB / ID: 8rwq
TitleKPC-2 G89D/E166Q Mutant Apo Structure
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / Beta-Lactamase / Inhibitor / Antibiotic Resistance
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase / beta-lactamase activity / response to antibiotic / Carbapenem-hydrolyzing beta-lactamase KPC-2
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 1.0Dec 25, 2024Provider: 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)31,3406
Polymers30,8641
Non-polymers4765
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-42 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.355, 78.659, 55.886
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-702-

HOH

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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 (E. coli) / References: UniProt: Q9F663, beta-lactamase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 42.77 %
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: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81531 Å / Relative weight: 1
ReflectionResolution: 1.05→45.56 Å / Num. obs: 124568 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 12.21 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 8.8
Reflection shellResolution: 1.05→1.07 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6156 / CC1/2: 0.32 / Rpim(I) all: 1.003

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→45.56 Å / SU ML: 0.151 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 6237 5.02 %
Rwork0.1486 118032 -
obs0.1496 124269 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.69 Å2
Refinement stepCycle: LAST / Resolution: 1.05→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 26 373 2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632160
X-RAY DIFFRACTIONf_angle_d0.90682957
X-RAY DIFFRACTIONf_chiral_restr0.0726329
X-RAY DIFFRACTIONf_plane_restr0.0152389
X-RAY DIFFRACTIONf_dihedral_angle_d12.9641781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.39011810.3943783X-RAY DIFFRACTION96.82
1.06-1.070.40312100.38143868X-RAY DIFFRACTION98.88
1.07-1.090.41352190.35653865X-RAY DIFFRACTION99.68
1.09-1.10.33922050.34943888X-RAY DIFFRACTION99.78
1.1-1.120.36052160.33373916X-RAY DIFFRACTION99.98
1.12-1.130.34061940.3193875X-RAY DIFFRACTION99.93
1.13-1.150.30442470.29873869X-RAY DIFFRACTION99.95
1.15-1.160.30232190.28443897X-RAY DIFFRACTION99.95
1.16-1.180.30781970.27293896X-RAY DIFFRACTION100
1.18-1.20.27972100.25543886X-RAY DIFFRACTION99.95
1.2-1.220.25782250.24213932X-RAY DIFFRACTION100
1.22-1.240.23721980.23443918X-RAY DIFFRACTION99.95
1.24-1.270.24082130.22333914X-RAY DIFFRACTION99.95
1.27-1.290.22931960.21273899X-RAY DIFFRACTION99.95
1.29-1.320.22211920.19033956X-RAY DIFFRACTION99.88
1.32-1.350.2171790.17843916X-RAY DIFFRACTION99.88
1.35-1.390.16771970.1653911X-RAY DIFFRACTION99.95
1.39-1.420.18731890.15263973X-RAY DIFFRACTION99.95
1.42-1.470.17152010.13933939X-RAY DIFFRACTION99.98
1.47-1.510.17121950.12853957X-RAY DIFFRACTION99.98
1.51-1.570.16442260.12213896X-RAY DIFFRACTION100
1.57-1.630.14972020.11333964X-RAY DIFFRACTION99.98
1.63-1.710.12952090.11013937X-RAY DIFFRACTION99.93
1.71-1.80.15041930.11163983X-RAY DIFFRACTION100
1.8-1.910.13291960.11113969X-RAY DIFFRACTION100
1.91-2.050.13632250.10713971X-RAY DIFFRACTION100
2.05-2.260.12432160.1093981X-RAY DIFFRACTION100
2.26-2.590.12412270.10774000X-RAY DIFFRACTION100
2.59-3.260.14062380.11964040X-RAY DIFFRACTION100
3.26-45.560.14812220.13734233X-RAY DIFFRACTION99.91

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