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- PDB-6qwb: Crystal structure of KPC-4 complexed with relebactam (16 hour soak) -

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Basic information

Entry
Database: PDB / ID: 6qwb
TitleCrystal structure of KPC-4 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
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: 1.04 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 20, 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)31,9208
Polymers30,8251
Non-polymers1,0957
Water7,332407
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-56 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.987, 79.150, 55.995
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-498-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 30824.627 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 (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: B1PL86, UniProt: Q9F663*PLUS, beta-lactamase

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Non-polymers , 5 types, 414 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M 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: 0.94 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: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.04→47.81 Å / Num. obs: 127468 / % possible obs: 99.4 % / Redundancy: 12.1 % / Rpim(I) all: 0.037 / Net I/σ(I): 12.7
Reflection shellResolution: 1.04→1.06 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5695 / Rpim(I) all: 0.481

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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→45.712 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 11.15
RfactorNum. reflection% reflection
Rfree0.1341 6468 5.07 %
Rwork0.1202 --
obs0.1209 127468 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.04→45.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 67 407 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122311
X-RAY DIFFRACTIONf_angle_d1.3453171
X-RAY DIFFRACTIONf_dihedral_angle_d17.588849
X-RAY DIFFRACTIONf_chiral_restr0.092345
X-RAY DIFFRACTIONf_plane_restr0.012418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.05180.19652030.20613615X-RAY DIFFRACTION90
1.0518-1.06420.20791980.19023848X-RAY DIFFRACTION96
1.0642-1.07720.20532180.19043955X-RAY DIFFRACTION98
1.0772-1.09080.182130.1673941X-RAY DIFFRACTION99
1.0908-1.10520.16052210.13984023X-RAY DIFFRACTION100
1.1052-1.12030.14552080.13383992X-RAY DIFFRACTION100
1.1203-1.13630.15812220.14063994X-RAY DIFFRACTION100
1.1363-1.15330.13972330.12194012X-RAY DIFFRACTION100
1.1533-1.17130.15422370.11733985X-RAY DIFFRACTION100
1.1713-1.19050.12632040.11014025X-RAY DIFFRACTION100
1.1905-1.2110.1292120.11364007X-RAY DIFFRACTION100
1.211-1.23310.13532090.12234001X-RAY DIFFRACTION100
1.2331-1.25680.13092240.1094079X-RAY DIFFRACTION100
1.2568-1.28240.10962030.10234047X-RAY DIFFRACTION100
1.2824-1.31030.14042430.11854007X-RAY DIFFRACTION100
1.3103-1.34080.11982000.10174042X-RAY DIFFRACTION100
1.3408-1.37430.11822170.09874035X-RAY DIFFRACTION100
1.3743-1.41150.12322070.09794055X-RAY DIFFRACTION100
1.4115-1.4530.1262080.09534032X-RAY DIFFRACTION100
1.453-1.49990.11232100.09034077X-RAY DIFFRACTION100
1.4999-1.55360.10292130.08734042X-RAY DIFFRACTION100
1.5536-1.61580.10542320.09054068X-RAY DIFFRACTION100
1.6158-1.68930.10292090.09114039X-RAY DIFFRACTION100
1.6893-1.77840.11742090.09484106X-RAY DIFFRACTION100
1.7784-1.88980.11992230.0994073X-RAY DIFFRACTION100
1.8898-2.03570.15362390.1184083X-RAY DIFFRACTION100
2.0357-2.24060.11972240.10724117X-RAY DIFFRACTION100
2.2406-2.56470.14722060.12334142X-RAY DIFFRACTION100
2.5647-3.23120.1372360.12894153X-RAY DIFFRACTION100
3.2312-45.75630.14321870.15164405X-RAY DIFFRACTION100

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