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- PDB-7qq5: Structure of CTX-M-15 K73A mutant crystallised in the presence of... -

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Basic information

Entry
Database: PDB / ID: 7qq5
TitleStructure of CTX-M-15 K73A mutant crystallised in the presence of enmetazobactam (AAI101)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / inhibitor / antibiotic resistance / cross-link
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae IS53 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: Mbio / Year: 2022
Title: Penicillanic Acid Sulfones Inactivate the Extended-Spectrum beta-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of beta-Lactamase Inhibition.
Authors: Hinchliffe, P. / Tooke, C.L. / Bethel, C.R. / Wang, B. / Arthur, C. / Heesom, K.J. / Shapiro, S. / Schlatzer, D.M. / Papp-Wallace, K.M. / Bonomo, R.A. / Spencer, J.
History
DepositionJan 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)28,6556
Polymers28,2351
Non-polymers4205
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.776, 45.465, 117.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 28234.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae IS53 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: W1EPV7, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0, 1 mM enmetazobactam

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.72 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 0.95→42.39 Å / Num. obs: 151225 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rpim(I) all: 0.05 / Net I/σ(I): 7.6
Reflection shellResolution: 0.95→0.97 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7432 / CC1/2: 0.357 / Rpim(I) all: 0.847 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QW8

6qw8


Resolution: 0.95→42.39 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1606 7514 4.98 %
Rwork0.1439 143344 -
obs0.1447 150858 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.85 Å2 / Biso mean: 12.562 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: final / Resolution: 0.95→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 21 336 2297
Biso mean--33.99 26.07 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.960.38932870.35224587487498
0.96-0.970.34762300.346747634993100
0.97-0.980.30842690.32147144983100
0.98-10.31492650.311347304995100
1-1.010.2682520.281646574909100
1.01-1.020.2552470.271947264973100
1.02-1.040.26712620.257447284990100
1.04-1.050.23442420.238647014943100
1.05-1.070.22522500.223747795029100
1.07-1.090.22452580.206947074965100
1.09-1.110.20072540.199547344988100
1.11-1.130.19922580.186847465004100
1.13-1.150.18092670.173947345001100
1.15-1.170.17982490.166547284977100
1.17-1.20.17382690.156947635032100
1.2-1.220.15992520.149147404992100
1.22-1.260.16682480.146747665014100
1.26-1.290.16282450.138147374982100
1.29-1.330.15632430.134147875030100
1.33-1.370.15792380.132947915029100
1.37-1.420.15633010.127647585059100
1.42-1.480.132420.115347755017100
1.48-1.540.12342450.105947935038100
1.54-1.620.13211910.106348705061100
1.62-1.730.12382750.104848135088100
1.73-1.860.12572530.104948065059100
1.86-2.050.10912360.100348755111100
2.05-2.340.11462330.103249115144100
2.34-2.950.13312410.113149355176100
2.95-42.390.15972120.145251905402100

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