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- PDB-6z22: Crystal structure of deacylation mutant KPC-4 (E166Q) -

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Basic information

Entry
Database: PDB / ID: 6z22
TitleCrystal structure of deacylation mutant KPC-4 (E166Q)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / unliganded beta-lactamase / 3-layer alpha-beta-alpha sandwich / part of the DD-peptidase and beta-lactamase superfamily.
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
beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3006
Polymers30,8241
Non-polymers4765
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-41 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.197, 78.941, 55.981
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-504-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30823.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC-4, blaKPC-2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1PL86, UniProt: Q9F663*PLUS, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
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: I04 / Wavelength: 0.77 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 1.4→45.66 Å / Num. obs: 53273 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rpim(I) all: 0.052 / Net I/σ(I): 8.8
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2586 / CC1/2: 0.674 / Rpim(I) all: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QWE

6qwe


Resolution: 1.4→45.66 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.26
RfactorNum. reflection% reflection
Rfree0.1763 2700 5.08 %
Rwork0.1398 --
obs0.1417 53103 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.19 Å2 / Biso mean: 23.7224 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 1.4→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 38 306 2343
Biso mean--35.27 35.01 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.29611340.238725992733100
1.43-1.450.29671450.216625732718100
1.45-1.480.25351280.208926582786100
1.48-1.510.22011360.179126182754100
1.51-1.550.20121340.174126392773100
1.55-1.590.19031590.160125992758100
1.59-1.630.21081490.153126062755100
1.63-1.680.19561460.141426312777100
1.68-1.730.19811510.14126102761100
1.73-1.80.19141510.133126392790100
1.8-1.870.17341460.126626442790100
1.87-1.950.18111320.15432631276399
1.95-2.060.14571360.121426532789100
2.06-2.180.19141240.122926652789100
2.18-2.350.17571630.13732641280499
2.35-2.590.16671340.117526912825100
2.59-2.960.15731300.122127142844100
2.97-3.740.15731550.127927282883100
3.74-45.660.15841470.146328643011100

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