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- PDB-6qw9: Crystal structure of KPC-2 complexed with relebactam (16 hour soak) -

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Basic information

Entry
Database: PDB / ID: 6qw9
TitleCrystal structure of KPC-2 complexed with relebactam (16 hour soak)
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / inhibitor / relebactam / diazabicyclooctane / antibiotic resistance.
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-JJT / Chem-MK7 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam.
Authors: Tooke, C.L. / Hinchliffe, P. / Lang, P.A. / Mulholland, A.J. / Brem, J. / Schofield, C.J. / Spencer, J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _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

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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)31,8067
Polymers30,8071
Non-polymers9996
Water6,287349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-36 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.925, 78.535, 55.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 30806.631 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 BL21(DE3) (bacteria) / References: UniProt: Q9F663, beta-lactamase

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Non-polymers , 5 types, 355 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: Chemical ChemComp-MK7 / (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide / MK-7655, bound form


Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-JJT / (2~{S})-5-azanylidene-2-(piperidin-4-ylcarbamoyl)piperidine-1-carboxylic acid


Mass: 268.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 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: I24 / Wavelength: 0.78 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: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.04→32.84 Å / Num. obs: 126716 / % possible obs: 100 % / Redundancy: 12.7 % / Rpim(I) all: 0.044 / Net I/σ(I): 10.5
Reflection shellResolution: 1.04→1.06 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6221 / Rpim(I) all: 0.774

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL8

5ul8


Resolution: 1.04→32.84 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 11.62
RfactorNum. reflection% reflection
Rfree0.1338 6309 4.98 %
Rwork0.1153 --
obs0.1162 126716 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.04→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 62 349 2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112302
X-RAY DIFFRACTIONf_angle_d1.3253163
X-RAY DIFFRACTIONf_dihedral_angle_d18.653846
X-RAY DIFFRACTIONf_chiral_restr0.094347
X-RAY DIFFRACTIONf_plane_restr0.013418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.05180.23222020.24843980X-RAY DIFFRACTION100
1.0518-1.06420.23562060.22763934X-RAY DIFFRACTION100
1.0642-1.07720.19822420.21073930X-RAY DIFFRACTION100
1.0772-1.09080.19372180.19733981X-RAY DIFFRACTION100
1.0908-1.10520.19152250.17543943X-RAY DIFFRACTION100
1.1052-1.12030.18352260.16413993X-RAY DIFFRACTION100
1.1203-1.13630.16122130.1553924X-RAY DIFFRACTION100
1.1363-1.15330.15572200.14263960X-RAY DIFFRACTION100
1.1533-1.17130.17012140.13913978X-RAY DIFFRACTION100
1.1713-1.19050.15372130.13533982X-RAY DIFFRACTION100
1.1905-1.2110.15172010.12643981X-RAY DIFFRACTION100
1.211-1.23310.13142100.12483960X-RAY DIFFRACTION100
1.2331-1.25680.1381790.12334007X-RAY DIFFRACTION100
1.2568-1.28240.14072170.11484021X-RAY DIFFRACTION100
1.2824-1.31030.13021740.10683978X-RAY DIFFRACTION100
1.3103-1.34080.1232180.10464008X-RAY DIFFRACTION100
1.3408-1.37430.12922240.10243968X-RAY DIFFRACTION100
1.3743-1.41150.12262350.09773998X-RAY DIFFRACTION100
1.4115-1.4530.10981700.09124041X-RAY DIFFRACTION100
1.453-1.49990.10812280.0873992X-RAY DIFFRACTION100
1.4999-1.55350.10622150.08374033X-RAY DIFFRACTION100
1.5535-1.61570.10042280.08243961X-RAY DIFFRACTION100
1.6157-1.68930.1092090.08054030X-RAY DIFFRACTION100
1.6893-1.77830.10071820.0874071X-RAY DIFFRACTION100
1.7783-1.88970.11642210.08664035X-RAY DIFFRACTION100
1.8897-2.03560.11021700.0944082X-RAY DIFFRACTION100
2.0356-2.24040.11012020.09714101X-RAY DIFFRACTION100
2.2404-2.56450.12081970.10214099X-RAY DIFFRACTION100
2.5645-3.23060.13482020.11644144X-RAY DIFFRACTION100
3.2306-32.86060.15462480.144292X-RAY DIFFRACTION100

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