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- PDB-6qwe: Crystal structure of KPC-4 -

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Basic information

Entry
Database: PDB / ID: 6qwe
TitleCrystal structure of KPC-4
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / serine beta-lactamase
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
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, 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 1.3Oct 16, 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)31,2976
Polymers30,8251
Non-polymers4725
Water5,008278
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-34 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.929, 78.737, 56.079
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-474-

HOH

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Components

#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
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
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: 0.94 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: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.4→45.68 Å / Num. obs: 52930 / % possible obs: 100 % / Redundancy: 12.6 % / Rpim(I) all: 0.074 / Net I/σ(I): 8.5
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2577 / Rpim(I) all: 1.019

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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: 1.4→45.68 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.67
RfactorNum. reflection% reflection
Rfree0.1767 2636 4.98 %
Rwork0.1453 --
obs0.1469 52930 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 27 278 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072153
X-RAY DIFFRACTIONf_angle_d0.9622943
X-RAY DIFFRACTIONf_dihedral_angle_d24.853771
X-RAY DIFFRACTIONf_chiral_restr0.072325
X-RAY DIFFRACTIONf_plane_restr0.007386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42550.26551780.26082561X-RAY DIFFRACTION100
1.4255-1.45290.26451600.23342578X-RAY DIFFRACTION100
1.4529-1.48260.24821340.21462596X-RAY DIFFRACTION100
1.4826-1.51480.22391360.2062626X-RAY DIFFRACTION100
1.5148-1.550.19671120.19372628X-RAY DIFFRACTION100
1.55-1.58880.22211160.18712629X-RAY DIFFRACTION100
1.5888-1.63180.17951170.17052639X-RAY DIFFRACTION100
1.6318-1.67980.21361280.16472641X-RAY DIFFRACTION100
1.6798-1.7340.21651340.15872618X-RAY DIFFRACTION100
1.734-1.7960.18811320.1532641X-RAY DIFFRACTION100
1.796-1.86790.17331650.13472635X-RAY DIFFRACTION100
1.8679-1.95290.15281530.1272593X-RAY DIFFRACTION100
1.9529-2.05590.13941410.11732650X-RAY DIFFRACTION100
2.0559-2.18470.16071360.12062637X-RAY DIFFRACTION100
2.1847-2.35330.1571330.11972691X-RAY DIFFRACTION100
2.3533-2.59010.14871290.12462668X-RAY DIFFRACTION100
2.5901-2.96490.1571330.12762696X-RAY DIFFRACTION100
2.9649-3.73520.15471270.13472749X-RAY DIFFRACTION100
3.7352-45.70190.1871720.14942818X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47961.198-0.32093.5015-0.50412.6946-0.08790.3446-0.0485-0.3430.0449-0.07920.03970.01560.02380.08510.0067-0.00980.1459-0.00710.08779.749214.7541-0.1741
21.41150.68891.66062.8858-1.3494.2639-0.1592-0.20960.1320.20770.07050.0948-0.5548-0.03760.07570.10470.02490.02570.1978-0.0470.127814.178126.607427.9817
34.4470.18191.61353.3016-0.48695.22860.078-0.1087-0.21970.03330.01620.01060.16210.0277-0.08390.072-0.0116-0.0050.1507-0.0060.076418.588716.185531.0231
41.4160.2402-0.23520.6384-0.06550.75120.0099-0.02870.0172-0.0006-0.0113-0.0474-0.01990.04910.00060.0768-0.0033-0.00440.10710.00340.078513.788418.090211.9673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 294 )

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