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- PDB-6xd7: KPC-2 N170A mutant bound to hydrolyzed ampicillin at 1.65 A -

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Basic information

Entry
Database: PDB / ID: 6xd7
TitleKPC-2 N170A mutant bound to hydrolyzed ampicillin at 1.65 A
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/Antibiotic / carbapenemase / beta-lactamase / antibiotic / HYDROLASE / HYDROLASE-Antibiotic complex
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
Chem-ZZ7 / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI032956 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: KPC-2 beta-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate.
Authors: Mehta, S.C. / Furey, I.M. / Pemberton, O.A. / Boragine, D.M. / Chen, Y. / Palzkill, T.
History
DepositionJun 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 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.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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

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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)31,5613
Polymers31,1011
Non-polymers4602
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.830, 59.380, 77.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

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


Mass: 31101.223 Da / Num. of mol.: 1 / Mutation: N170A
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-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→36.26 Å / Num. obs: 31981 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.65-1.687.12.6561097615560.3991.599.3
9.04-36.265.80.08514212470.99515.498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.44 Å36.26 Å
Translation5.44 Å36.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.1data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
iMOSFLM7.3.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL8

5ul8


Resolution: 1.65→36.26 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3132 5.2 %
Rwork0.1564 57127 -
obs0.1591 31931 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.38 Å2 / Biso mean: 30.5415 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 1.65→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 31 149 2163
Biso mean--38.49 42.73 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.3751230.27752572269598
1.68-1.70.27881360.27772577271399
1.7-1.730.33511230.26972641276499
1.73-1.760.35141380.25472578271699
1.76-1.80.31361360.23192620275699
1.8-1.830.29711580.20992548270698
1.83-1.870.24481400.19842578271898
1.87-1.920.25541470.18626002747100
1.92-1.970.23041320.16426292761100
1.97-2.020.25161610.161525912752100
2.02-2.080.22381060.148426372743100
2.08-2.150.22131570.145526032760100
2.15-2.220.19631430.132526342777100
2.22-2.310.18641410.14142581272299
2.31-2.420.20261460.13982592273899
2.42-2.540.17391470.14042586273399
2.54-2.70.19671560.152564272098
2.7-2.910.21071730.149225742747100
2.91-3.210.19531500.156326052755100
3.21-3.670.18321240.136426382762100
3.67-4.620.15051470.129526222769100
4.62-36.260.21711480.16312557270598

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