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- PDB-6z21: Crystal structure of deacylation mutant KPC-2 (E166Q) -

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Basic information

Entry
Database: PDB / ID: 6z21
TitleCrystal structure of deacylation mutant KPC-2 (E166Q)
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / antibiotic resistance / mutant / carbapenemase.
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T016035/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance.
Authors: Tooke, C.L. / Hinchliffe, P. / Bonomo, R.A. / Schofield, C.J. / Mulholland, A.J. / Spencer, J.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,60210
Polymers30,8061
Non-polymers7969
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-79 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.200, 78.440, 55.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-305-

SO4

21A-466-

HOH

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 30805.646 Da / Num. of mol.: 1 / Mutation: E166Q
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.8M ammonium sulphate, 5% ethanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.93998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93998 Å / Relative weight: 1
ReflectionResolution: 1.3→45.56 Å / Num. obs: 65868 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 11.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 12.2 / Num. unique obs: 3241 / CC1/2: 0.46 / Rpim(I) all: 0.686 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QW9

6qw9


Resolution: 1.3→32.861 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 3316 5.04 %
Rwork0.143 62477 -
obs0.1446 65793 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.65 Å2 / Biso mean: 25.2192 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: final / Resolution: 1.3→32.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 73 230 2319
Biso mean--46.64 39.13 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.3-1.31860.39331240.34922558
1.3186-1.33830.35351400.32232600
1.3383-1.35920.33371270.31062541
1.3592-1.38150.31831120.29212602
1.3815-1.40530.2631350.27612575
1.4053-1.43080.29341050.25222606
1.4308-1.45830.30221440.23692566
1.4583-1.48810.30921400.23292554
1.4881-1.52050.27751450.22142587
1.5205-1.55580.23811450.19622590
1.5558-1.59470.19321460.15832546
1.5947-1.63790.20981530.14572586
1.6379-1.68610.17121380.13032572
1.6861-1.74050.15911220.12842603
1.7405-1.80270.17391290.12792615
1.8027-1.87480.16221480.1192582
1.8748-1.96020.13561470.10482593
1.9602-2.06350.15611250.10382628
2.0635-2.19280.13211630.1092580
2.1928-2.3620.17311520.11212617
2.362-2.59960.12791380.11512628
2.5996-2.97560.17511400.12512656
2.9756-3.74810.14491490.12952685
3.7481-32.8610.16331490.14962807

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