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- PDB-7r3q: Crystal structure of CTX-M-15 G238C/A240 insert mutant apoenzyme -

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Basic information

Entry
Database: PDB / ID: 7r3q
TitleCrystal structure of CTX-M-15 G238C/A240 insert 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 / FOURIER SYNTHESIS / Resolution: 1.46 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
DepositionFeb 7, 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 1.4Oct 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)28,8306
Polymers28,4101
Non-polymers4205
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-23 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.475, 45.583, 117.900
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: 28410.160 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-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.: 380 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.73379 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73379 Å / Relative weight: 1
ReflectionResolution: 1.456→58.95 Å / Num. obs: 42845 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 13.66 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.097 / Net I/σ(I): 6.1
Reflection shellResolution: 1.456→1.481 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2124 / CC1/2: 0.419 / Rpim(I) all: 1.268 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HBT

4hbt


Resolution: 1.46→58.95 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 2107 4.92 %
Rwork0.1569 40726 -
obs0.1595 42833 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.06 Å2
Refinement stepCycle: LAST / Resolution: 1.46→58.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 21 380 2370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872092
X-RAY DIFFRACTIONf_angle_d0.9992856
X-RAY DIFFRACTIONf_chiral_restr0.0764331
X-RAY DIFFRACTIONf_plane_restr0.0069375
X-RAY DIFFRACTIONf_dihedral_angle_d17.808785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.37031740.27342639X-RAY DIFFRACTION99.96
1.49-1.530.35231200.25272684X-RAY DIFFRACTION99.96
1.53-1.570.26881260.23852689X-RAY DIFFRACTION100
1.57-1.610.31381210.2232690X-RAY DIFFRACTION100
1.61-1.670.31311270.21392688X-RAY DIFFRACTION99.93
1.67-1.730.2891290.19992698X-RAY DIFFRACTION99.89
1.73-1.80.25941400.17112672X-RAY DIFFRACTION100
1.8-1.880.24911700.15842671X-RAY DIFFRACTION99.96
1.88-1.980.2111560.152688X-RAY DIFFRACTION100
1.98-2.10.21221510.13892686X-RAY DIFFRACTION100
2.1-2.260.20061540.13232704X-RAY DIFFRACTION99.97
2.26-2.490.20151420.12532728X-RAY DIFFRACTION100
2.49-2.850.20461310.14342761X-RAY DIFFRACTION100
2.85-3.590.15341470.13792772X-RAY DIFFRACTION100
3.59-58.950.16251190.14432956X-RAY DIFFRACTION99.9

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