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- PDB-6qwa: Crystal structure of KPC-3 complexed with relebactam (16 hour soak) -

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Basic information

Entry
Database: PDB / ID: 6qwa
TitleCrystal structure of KPC-3 complexed with relebactam (16 hour soak)
ComponentsBeta-lactamase
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
ETHANOL / Chem-JJT / Chem-MK7 / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7817
Polymers30,8321
Non-polymers9496
Water6,720373
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-31 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.128, 78.717, 55.806
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 Beta-lactamase


Mass: 30831.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, blaKPC-3, kpc3, DXF97_27070 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q93DC4, UniProt: Q9F663*PLUS, beta-lactamase

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Non-polymers , 6 types, 379 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: 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
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
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: I04 / Wavelength: 0.86 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.06→60.13 Å / Num. obs: 118930 / % possible obs: 98.9 % / Redundancy: 13.1 % / Rpim(I) all: 0.033 / Net I/σ(I): 14
Reflection shellResolution: 1.06→1.08 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5730 / Rpim(I) all: 0.454

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Processing

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

5ul8


Resolution: 1.06→55.806 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.6
RfactorNum. reflection% reflection
Rfree0.1425 5987 5.03 %
Rwork0.1212 --
obs0.1223 118930 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.06→55.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 60 373 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012225
X-RAY DIFFRACTIONf_angle_d1.3573047
X-RAY DIFFRACTIONf_dihedral_angle_d13.231812
X-RAY DIFFRACTIONf_chiral_restr0.098341
X-RAY DIFFRACTIONf_plane_restr0.013400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.0720.22781870.20273686X-RAY DIFFRACTION97
1.072-1.08470.22641720.18953653X-RAY DIFFRACTION97
1.0847-1.09790.19062130.17183660X-RAY DIFFRACTION97
1.0979-1.11180.17491660.15673697X-RAY DIFFRACTION97
1.1118-1.12640.15991840.1523682X-RAY DIFFRACTION98
1.1264-1.14190.15261910.14133703X-RAY DIFFRACTION98
1.1419-1.15820.17171920.13213715X-RAY DIFFRACTION98
1.1582-1.17550.14611910.13083668X-RAY DIFFRACTION98
1.1755-1.19380.16122050.12623702X-RAY DIFFRACTION98
1.1938-1.21340.13671820.12473725X-RAY DIFFRACTION98
1.2134-1.23430.13382050.11693709X-RAY DIFFRACTION98
1.2343-1.25680.1391860.11533709X-RAY DIFFRACTION98
1.2568-1.28090.13761770.11243745X-RAY DIFFRACTION98
1.2809-1.30710.14772020.11193764X-RAY DIFFRACTION99
1.3071-1.33550.12161950.10763722X-RAY DIFFRACTION99
1.3355-1.36660.13781940.10423774X-RAY DIFFRACTION99
1.3666-1.40080.12632020.10293745X-RAY DIFFRACTION99
1.4008-1.43860.12462040.09673774X-RAY DIFFRACTION99
1.4386-1.4810.11711720.09533806X-RAY DIFFRACTION99
1.481-1.52880.10962010.08853754X-RAY DIFFRACTION99
1.5288-1.58340.12292330.09363774X-RAY DIFFRACTION99
1.5834-1.64680.1021860.08883806X-RAY DIFFRACTION100
1.6468-1.72180.1072170.09223792X-RAY DIFFRACTION100
1.7218-1.81260.11552220.09863796X-RAY DIFFRACTION100
1.8126-1.92610.11942230.10523829X-RAY DIFFRACTION100
1.9261-2.07490.12592100.10723834X-RAY DIFFRACTION100
2.0749-2.28370.12382140.11093838X-RAY DIFFRACTION100
2.2837-2.61410.14781890.1183917X-RAY DIFFRACTION100
2.6141-3.29350.15582370.13573897X-RAY DIFFRACTION100
3.2935-55.88350.17692350.15194067X-RAY DIFFRACTION100

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