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- PDB-6z7j: Structure of CTX-M-15 crystallised in the presence of enmetazobac... -

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Basic information

Entry
Database: PDB / ID: 6z7j
TitleStructure of CTX-M-15 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 activity / beta-lactamase / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae IS53 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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
DepositionMay 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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)28,6015
Polymers28,2771
Non-polymers3244
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-23 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.806, 45.994, 118.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 28276.986 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) / Variant (production host): SoluBL21 / References: UniProt: W1EPV7, 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-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.: 364 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0, 10mM enmetazobactam (AAI101)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.14→45.99 Å / Num. obs: 91464 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 7.72 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.048 / Net I/σ(I): 8.4
Reflection shellResolution: 1.14→1.15 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4448 / CC1/2: 0.74 / Rpim(I) all: 0.538 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QW8

6qw8


Resolution: 1.14→41.92 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.152 4481 4.91 %
Rwork0.1386 86847 -
obs0.1393 91328 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 13.7724 Å2 / Biso min: 5.53 Å2
Refinement stepCycle: final / Resolution: 1.14→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 16 364 2323
Biso mean--40.2 27.58 -
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 (%)
1.14-1.150.38711490.37492853300299
1.15-1.160.32671610.30892798295999
1.16-1.180.27221480.251928693017100
1.18-1.190.22721460.20372826297299
1.19-1.210.20791540.17628643018100
1.21-1.220.21351460.17162806295299
1.22-1.240.17831470.157728933040100
1.24-1.260.19771430.16082848299199
1.26-1.280.19121430.163228923035100
1.28-1.30.17531520.16328092961100
1.3-1.320.15261640.150728823046100
1.32-1.350.14781380.124328633001100
1.35-1.370.16451600.126528603020100
1.37-1.40.16351380.125329263064100
1.4-1.430.12291270.122328722999100
1.43-1.460.13391540.12828653019100
1.46-1.50.15581510.125828913042100
1.5-1.540.13991450.121928953040100
1.54-1.590.141590.116628833042100
1.59-1.640.14731530.118428763029100
1.64-1.70.13691830.118228693052100
1.7-1.760.14041400.117129193059100
1.76-1.840.13761210.116829463067100
1.84-1.940.12691360.123729183054100
1.94-2.060.12521530.120729183071100
2.06-2.220.13431540.118829433097100
2.22-2.450.12651440.117229443088100
2.45-2.80.1361400.129129923132100
2.8-3.530.13731640.137629863150100
3.53-41.920.15371680.15331413309100

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