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- PDB-7qqc: Structure of CTX-M-15 K73A mutant -

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Basic information

Entry
Database: PDB / ID: 7qqc
TitleStructure of CTX-M-15 K73A mutant
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / mutant / antibiotic resistance
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 / 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 / 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 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

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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)28,6556
Polymers28,2351
Non-polymers4205
Water6,395355
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)44.896, 45.552, 116.705
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: 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.: 355 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 294.15 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: 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→42.43 Å / Num. obs: 151252 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 8.53 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 8.2
Reflection shellResolution: 0.95→0.97 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7462 / CC1/2: 0.368 / Rpim(I) all: 0.794 / % possible all: 99.9

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Processing

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

6qw8


Resolution: 0.95→35.91 Å / SU ML: 0.1232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1555 7641 5.06 %
Rwork0.1397 143233 -
obs0.1405 150874 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.51 Å2
Refinement stepCycle: LAST / Resolution: 0.95→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 21 355 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612082
X-RAY DIFFRACTIONf_angle_d1.00332844
X-RAY DIFFRACTIONf_chiral_restr0.0792326
X-RAY DIFFRACTIONf_plane_restr0.0071377
X-RAY DIFFRACTIONf_dihedral_angle_d16.3527780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.34772540.35964685X-RAY DIFFRACTION99.8
0.96-0.970.34892310.34654776X-RAY DIFFRACTION99.96
0.97-0.980.33172410.33854724X-RAY DIFFRACTION99.8
0.98-10.3232850.31744694X-RAY DIFFRACTION99.66
1-1.010.28472550.28364691X-RAY DIFFRACTION99.64
1.01-1.020.29372720.27774706X-RAY DIFFRACTION99.58
1.02-1.040.25642540.25384730X-RAY DIFFRACTION99.6
1.04-1.050.25562380.23454693X-RAY DIFFRACTION99.54
1.05-1.070.23162420.21544765X-RAY DIFFRACTION99.72
1.07-1.090.2272220.19994742X-RAY DIFFRACTION99.7
1.09-1.110.19932720.194737X-RAY DIFFRACTION99.78
1.11-1.130.19672360.18034717X-RAY DIFFRACTION99.76
1.13-1.150.18912840.17324730X-RAY DIFFRACTION99.78
1.15-1.170.18852510.17154761X-RAY DIFFRACTION99.78
1.17-1.20.17452530.16024720X-RAY DIFFRACTION99.82
1.2-1.220.15632270.14054776X-RAY DIFFRACTION99.76
1.22-1.260.16642530.1354774X-RAY DIFFRACTION99.72
1.26-1.290.1392500.12614741X-RAY DIFFRACTION99.9
1.29-1.330.14282580.12224745X-RAY DIFFRACTION99.8
1.33-1.370.14322750.12074753X-RAY DIFFRACTION99.86
1.37-1.420.13322480.11474801X-RAY DIFFRACTION99.9
1.42-1.480.13052980.11214722X-RAY DIFFRACTION99.92
1.48-1.540.1262270.1064824X-RAY DIFFRACTION99.96
1.54-1.620.13912460.09734835X-RAY DIFFRACTION99.94
1.62-1.730.12192060.09734854X-RAY DIFFRACTION99.98
1.73-1.860.11852760.09884794X-RAY DIFFRACTION99.98
1.86-2.050.11372610.09684850X-RAY DIFFRACTION100
2.05-2.340.11442730.10134857X-RAY DIFFRACTION99.98
2.34-2.950.11762810.11694901X-RAY DIFFRACTION100
2.95-35.910.16632720.14515135X-RAY DIFFRACTION99.87

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