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- PDB-7q0z: Crystal structure of CTX-M-14 -

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Basic information

Entry
Database: PDB / ID: 7q0z
TitleCrystal structure of CTX-M-14
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase / Antibiotic / Resistence
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsWerner, N. / Perbandt, M. / Hinrichs, W. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Sci Rep / Year: 2022
Title: Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as beta-lactamase inhibitors.
Authors: Perbandt, M. / Werner, N. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Hinrichs, W. / Betzel, C.
History
DepositionOct 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6459
Polymers27,8881
Non-polymers7578
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-41 kcal/mol
Surface area11380 Å2
Unit cell
Length a, b, c (Å)41.361, 62.497, 86.421
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: 27888.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30 % PEG8000, 0.2 M lithium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1→29.88 Å / Num. obs: 121023 / % possible obs: 99.63 % / Redundancy: 12.1 % / Biso Wilson estimate: 7.02 Å2 / CC1/2: 1 / Rrim(I) all: 0.038 / Net I/σ(I): 36.49
Reflection shellResolution: 1→1.04 Å / Mean I/σ(I) obs: 7.83 / Num. unique obs: 11775 / CC1/2: 0.982 / Rrim(I) all: 0.247

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTH

6gth


Resolution: 1→23.96 Å / SU ML: 0.0733 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.3359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1719 6051 5 %
Rwork0.1596 114969 -
obs0.1602 121020 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.43 Å2
Refinement stepCycle: LAST / Resolution: 1→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 43 478 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082149
X-RAY DIFFRACTIONf_angle_d1.10532951
X-RAY DIFFRACTIONf_chiral_restr0.0845343
X-RAY DIFFRACTIONf_plane_restr0.0127386
X-RAY DIFFRACTIONf_dihedral_angle_d7.5756323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.23881860.21633527X-RAY DIFFRACTION92.55
1.01-1.020.20941990.20563792X-RAY DIFFRACTION99.97
1.02-1.040.20922020.19483826X-RAY DIFFRACTION99.9
1.04-1.050.19221980.19853766X-RAY DIFFRACTION99.95
1.05-1.060.2012020.19453834X-RAY DIFFRACTION99.93
1.06-1.080.18461990.19223774X-RAY DIFFRACTION99.82
1.08-1.090.19611980.1893766X-RAY DIFFRACTION99
1.09-1.110.18162000.18693813X-RAY DIFFRACTION99.98
1.11-1.130.17752010.17793817X-RAY DIFFRACTION100
1.13-1.140.21182010.183822X-RAY DIFFRACTION99.95
1.14-1.160.2152000.17983798X-RAY DIFFRACTION100
1.16-1.190.1942030.17643851X-RAY DIFFRACTION100
1.19-1.210.1941990.18073777X-RAY DIFFRACTION99.65
1.21-1.230.19171990.18083783X-RAY DIFFRACTION99.03
1.23-1.260.21652020.18093834X-RAY DIFFRACTION100
1.26-1.290.17642010.17393820X-RAY DIFFRACTION100
1.29-1.320.1872010.17043814X-RAY DIFFRACTION100
1.32-1.360.19152020.16973839X-RAY DIFFRACTION99.95
1.36-1.40.17882010.1723832X-RAY DIFFRACTION99.83
1.4-1.440.19232030.16013848X-RAY DIFFRACTION99.78
1.44-1.490.17062000.15933810X-RAY DIFFRACTION99.33
1.49-1.550.14982020.15723827X-RAY DIFFRACTION100
1.55-1.620.15992040.15383888X-RAY DIFFRACTION100
1.62-1.710.17992040.15343871X-RAY DIFFRACTION100
1.71-1.820.16812030.15443853X-RAY DIFFRACTION100
1.82-1.960.17892050.15023892X-RAY DIFFRACTION99.93
1.96-2.150.15512040.13913877X-RAY DIFFRACTION99.71
2.15-2.460.15052060.13863919X-RAY DIFFRACTION100
2.47-3.10.15722090.1413969X-RAY DIFFRACTION99.95
3.1-23.960.14732170.14784130X-RAY DIFFRACTION99.89

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