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- PDB-7ua7: Crystal structure of indoline 9 with KPC-2 -

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Basic information

Entry
Database: PDB / ID: 7ua7
TitleCrystal structure of indoline 9 with KPC-2
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / beta-lactamase / tetrazole / inhibitor / complex
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, 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-M53 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.247 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161762 United States
CitationJournal: To Be Published
Title: Probing the binding hot spots of KPC-2 carbapenemase using reversible tetrazole-based inhibitors
Authors: DeFrees, K. / Cambeis, E.M. / Chen, Y. / Renslo, A.R.
History
DepositionMar 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5835
Polymers28,7891
Non-polymers7944
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.844, 58.747, 76.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 28789.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F663, 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-M53 / tert-butyl {(3R)-3-[(1H-tetrazol-5-yl)carbamoyl]-1-[3-(trifluoromethyl)benzoyl]-2,3-dihydro-1H-indol-3-yl}carbamate


Mass: 517.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22F3N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium Sulfate, 5%(v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.247→50 Å / Num. obs: 12678 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Χ2: 0.915 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.296.10.3666100.960.1580.40.99298.9
2.29-2.336.40.3646270.9430.1540.3961.00899.5
2.33-2.386.60.356150.9380.1460.380.975100
2.38-2.426.90.3265950.9420.1340.3530.954100
2.42-2.487.10.36530.9650.1210.3241.032100
2.48-2.537.30.2786020.9670.1120.31.078100
2.53-2.67.20.2456320.9750.0990.2651.035100
2.6-2.677.30.2276280.9770.090.2451.031100
2.67-2.757.30.2016100.9760.080.2171.042100
2.75-2.837.20.1826410.9830.0730.1971.025100
2.83-2.947.30.1716210.9810.0690.1850.992100
2.94-3.057.20.1546250.9890.0620.1661.02100
3.05-3.197.20.1326360.9880.0520.1420.988100
3.19-3.367.20.1146200.9930.0470.1230.964100
3.36-3.577.20.1016480.9930.040.1090.915100
3.57-3.857.20.0916410.9910.0370.0980.86100
3.85-4.237.10.086340.9950.0320.0860.759100
4.23-4.857.10.0716600.9930.0290.0760.676100
4.85-6.170.0646560.9960.0260.070.569100
6.1-506.40.0537240.9950.0220.0570.428100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.6 Å46.55 Å
Translation5.6 Å46.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 2.247→46.546 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1230 10.04 %
Rwork0.1766 11021 -
obs0.1818 12251 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.75 Å2 / Biso mean: 31.2387 Å2 / Biso min: 15.28 Å2
Refinement stepCycle: final / Resolution: 2.247→46.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 55 80 2152
Biso mean--48.51 33.46 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2474-2.33740.25881150.195799580
2.3374-2.44380.27821200.1839112891
2.4438-2.57260.27011370.184121998
2.5726-2.73380.21951410.18471244100
2.7338-2.94480.23091370.19351256100
2.9448-3.24110.24551380.20191255100
3.2411-3.70990.2121400.17051277100
3.7099-4.67340.21641410.15071293100
4.6734-46.540.22041610.17641354100

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