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- PDB-6z7i: Crystal structure of CTX-M-15 E166Q mutant apoenzyme -

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Basic information

Entry
Database: PDB / ID: 6z7i
TitleCrystal structure of CTX-M-15 E166Q mutant apoenzyme
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 / membrane
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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

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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)28,7686
Polymers28,2921
Non-polymers4765
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-35 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.587, 45.693, 117.606
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: 28292.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 42.92 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0, 2.0 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.72 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 0.98→45.69 Å / Num. obs: 138530 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 8.02 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.051 / Net I/σ(I): 7.6
Reflection shellResolution: 0.98→1 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6818 / CC1/2: 0.487 / Rpim(I) all: 0.649 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QW8

6qw8


Resolution: 0.98→42.59 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1442 7006 5.07 %
Rwork0.1264 131164 -
obs0.1273 138170 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.48 Å2 / Biso mean: 12.9246 Å2 / Biso min: 4.01 Å2
Refinement stepCycle: final / Resolution: 0.98→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 39 363 2347
Biso mean--29.34 29.58 -
Num. residues----260
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 (%)
0.98-0.990.28132410.273143344575100
0.99-10.25582560.246842454501100
1-1.020.2482250.24084366459199
1.02-1.030.24952520.220842584510100
1.03-1.040.22542520.218443034555100
1.04-1.060.22482440.212142834527100
1.06-1.070.21112230.190743514574100
1.07-1.090.19592160.175143554571100
1.09-1.10.19731870.161543614548100
1.1-1.120.17451970.149743464543100
1.12-1.140.14062460.13543674613100
1.14-1.160.14192340.132143014535100
1.16-1.180.14492260.127843104536100
1.18-1.210.14172460.125343754621100
1.21-1.230.1352270.119143474574100
1.23-1.260.14672320.120943224554100
1.26-1.30.1462730.11143084581100
1.3-1.330.12122080.112543884596100
1.33-1.370.14052550.105643414596100
1.37-1.410.12172330.09843854618100
1.41-1.460.1382220.099143644586100
1.46-1.520.11062220.091844174639100
1.52-1.590.10232280.095944084636100
1.59-1.680.13062650.094443414606100
1.68-1.780.1042350.098544164651100
1.78-1.920.10362470.101444024649100
1.92-2.110.12341960.100344714667100
2.11-2.420.12372270.104644824709100
2.42-3.040.12432430.122945134756100
3.05-42.590.17142480.147547044952100

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