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- PDB-5ll7: Crystal structure of KPC-2 carbapenemase in complex with a phenyl... -

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Basic information

Entry
Database: PDB / ID: 5ll7
TitleCrystal structure of KPC-2 carbapenemase in complex with a phenyl boronic inhibitor.
ComponentsBeta-lactamase
KeywordsHYDROLASE / carbapenemase / beta-lactamase / phenyl boronic inhibitor
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6YV / beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVicario, M. / Celenza, G. / Bellio, P. / Perilli, M.G. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondo Ateneo Ricerca University of Modena and Reggio Emilia Italy
CitationJournal: Chemmedchem / Year: 2018
Title: Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance.
Authors: Celenza, G. / Vicario, M. / Bellio, P. / Linciano, P. / Perilli, M. / Oliver, A. / Blazquez, J. / Cendron, L. / Tondi, D.
History
DepositionJul 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7695
Polymers28,3911
Non-polymers3784
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint6 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.033, 65.764, 72.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Kpc-2 carbapenemase


Mass: 28390.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaKPC-18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H4IUK8, beta-lactamase
#2: Chemical ChemComp-6YV / (~{E})-3-[2-(dihydroxyboranyl)phenyl]prop-2-enoic acid


Mass: 191.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9BO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15% polyethylene glycol 6000 (PEG 6000), 200mM potassium thiocyanate (KSCN), 100 mM sodium citrate (pH 4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.4→40.565 Å / Num. obs: 46694 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.4→40.565 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs45709 98.2 %
Refinement stepCycle: LAST / Resolution: 1.4→40.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 26 154 2152

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