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- PDB-7q11: Crystal structure of CTX-M-14 in complex with Ixazomib -

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Basic information

Entry
Database: PDB / ID: 7q11
TitleCrystal structure of CTX-M-14 in complex with Ixazomib
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
Chem-6V8 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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
Revision 1.2Nov 6, 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)29,17413
Polymers27,8881
Non-polymers1,28512
Water7,062392
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.485, 62.372, 87.187
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 404 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-6V8 / [(1~{R})-1-[2-[[2,5-bis(chloranyl)phenyl]carbonylamino]ethanoylamino]-3-methyl-butyl]boronic acid


Mass: 361.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19BCl2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.18 %
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: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.14→37.46 Å / Num. obs: 83198 / % possible obs: 99.98 % / Redundancy: 12.4 % / Biso Wilson estimate: 8.08 Å2 / CC1/2: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 29.01
Reflection shellResolution: 1.14→1.18 Å / Mean I/σ(I) obs: 8.06 / Num. unique obs: 8214 / CC1/2: 0.982 / Rrim(I) all: 0.263

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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: 1.14→43.59 Å / SU ML: 0.0596 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.7303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1432 2101 2.52 %
Rwork0.1314 81136 -
obs0.1318 83237 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.17 Å2
Refinement stepCycle: LAST / Resolution: 1.14→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 70 392 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762158
X-RAY DIFFRACTIONf_angle_d1.18662960
X-RAY DIFFRACTIONf_chiral_restr0.083342
X-RAY DIFFRACTIONf_plane_restr0.0151386
X-RAY DIFFRACTIONf_dihedral_angle_d9.343321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.16851370.13445289X-RAY DIFFRACTION98.94
1.17-1.20.15221390.13115355X-RAY DIFFRACTION100
1.2-1.230.13521380.12875348X-RAY DIFFRACTION99.96
1.23-1.260.1611390.12555353X-RAY DIFFRACTION100
1.26-1.30.14071390.12355360X-RAY DIFFRACTION100
1.3-1.350.14351380.12425338X-RAY DIFFRACTION100
1.35-1.410.16041390.12785374X-RAY DIFFRACTION100
1.41-1.470.12821400.12125392X-RAY DIFFRACTION100
1.47-1.550.14891390.12015383X-RAY DIFFRACTION100
1.55-1.640.13421400.12295401X-RAY DIFFRACTION99.98
1.64-1.770.14441400.12855404X-RAY DIFFRACTION99.96
1.77-1.950.14281400.12455446X-RAY DIFFRACTION100
1.95-2.230.12891420.11865459X-RAY DIFFRACTION99.98
2.23-2.810.12591420.13525509X-RAY DIFFRACTION100
2.81-43.590.15491490.14925725X-RAY DIFFRACTION99.93

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