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- PDB-6z7k: Crystal structure of CTX-M-15 in complex with the imine form of h... -

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Basic information

Entry
Database: PDB / ID: 6z7k
TitleCrystal structure of CTX-M-15 in complex with the imine form of hydrolysed tazobactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / inhibitor / antibiotic resistance
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QBZ / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.3Nov 20, 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)28,8385
Polymers28,2931
Non-polymers5454
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-23 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.693, 45.426, 117.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Plasmid: pOPIN-F / Production host: Escherichia coli (E. coli) / Variant (production host): SoluBL21 / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-QBZ / (2~{S},3~{S})-3-[bis(oxidanylidene)-$l^{5}-sulfanyl]-3-methyl-2-[(~{E})-3-oxidanylidenepropylideneamino]-4-(1,2,3-triaz ol-1-yl)butanoic acid / Tazobactam imine intermediate


Mass: 317.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.82 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 1.1→58.88 Å / Num. obs: 98191 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 10.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 12.9
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4809 / CC1/2: 0.787 / Rpim(I) all: 0.388

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Processing

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

6qw8


Resolution: 1.1→58.88 Å / SU ML: 0.0855 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1438 5001 5.1 %
Rwork0.1292 93081 -
obs0.13 98082 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.13 Å2
Refinement stepCycle: LAST / Resolution: 1.1→58.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 31 291 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782113
X-RAY DIFFRACTIONf_angle_d1.07632884
X-RAY DIFFRACTIONf_chiral_restr0.0837333
X-RAY DIFFRACTIONf_plane_restr0.0084383
X-RAY DIFFRACTIONf_dihedral_angle_d18.1066791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.24431500.22723085X-RAY DIFFRACTION100
1.11-1.130.22771950.20143008X-RAY DIFFRACTION100
1.13-1.140.21171720.19113084X-RAY DIFFRACTION100
1.14-1.150.17531610.18183051X-RAY DIFFRACTION99.97
1.15-1.170.19241540.17763071X-RAY DIFFRACTION100
1.17-1.180.18691730.1693044X-RAY DIFFRACTION100
1.18-1.20.18011630.16323109X-RAY DIFFRACTION100
1.2-1.220.19871440.15713085X-RAY DIFFRACTION100
1.22-1.240.17561500.15353073X-RAY DIFFRACTION100
1.24-1.260.1861740.14673047X-RAY DIFFRACTION100
1.26-1.280.15371660.14083093X-RAY DIFFRACTION100
1.28-1.30.16361810.14083059X-RAY DIFFRACTION100
1.3-1.330.15641680.13563069X-RAY DIFFRACTION100
1.33-1.360.1641750.13223095X-RAY DIFFRACTION100
1.36-1.390.15551610.13213085X-RAY DIFFRACTION99.97
1.39-1.420.15011480.12573118X-RAY DIFFRACTION99.97
1.42-1.450.14721650.11973058X-RAY DIFFRACTION100
1.45-1.490.13481580.11363092X-RAY DIFFRACTION99.97
1.49-1.540.1432040.11433053X-RAY DIFFRACTION99.91
1.54-1.590.12351520.10853102X-RAY DIFFRACTION99.97
1.59-1.640.14131620.10713098X-RAY DIFFRACTION99.85
1.64-1.710.12171630.10663107X-RAY DIFFRACTION99.97
1.71-1.790.11761630.10723135X-RAY DIFFRACTION100
1.79-1.880.11351780.10533104X-RAY DIFFRACTION100
1.88-20.11741760.10183118X-RAY DIFFRACTION100
2-2.150.13061800.10343117X-RAY DIFFRACTION100
2.15-2.370.13051720.10713150X-RAY DIFFRACTION100
2.37-2.710.12831600.11523174X-RAY DIFFRACTION100
2.71-3.420.14551740.13093210X-RAY DIFFRACTION100
3.42-58.880.15011590.15813387X-RAY DIFFRACTION99.97

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