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- PDB-7u9b: Crystal structure of indoline 7 with KPC-2 -

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Basic information

Entry
Database: PDB / ID: 7u9b
TitleCrystal structure of indoline 7 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-M2I / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 10, 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 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: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8092
Polymers28,4501
Non-polymers3591
Water2,018112
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)56.710, 58.910, 76.660
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-433-

HOH

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Components

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


Mass: 28450.090 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-M2I / [(3S)-3-(1H-tetrazol-5-yl)-2,3-dihydro-1H-indol-1-yl][3-(trifluoromethyl)phenyl]methanone


Mass: 359.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12F3N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 46.36 %
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: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→36.055 Å / Num. obs: 37090 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-23.60.723947326170.7492.1100
8.94-36.053.30.04913884210.9961498.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.61 Å36.05 Å
Translation5.61 Å36.05 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.95→36.055 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 926 4.79 %
Rwork0.1786 18398 -
obs0.1809 19324 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.99 Å2 / Biso mean: 25.4387 Å2 / Biso min: 8.03 Å2
Refinement stepCycle: final / Resolution: 1.95→36.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 26 112 2140
Biso mean--37.18 32.19 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.95-2.05280.28721290.22132578
2.0528-2.18140.25471250.20062590
2.1814-2.34980.2881180.18952600
2.3498-2.58620.23591200.18152606
2.5862-2.96030.21161450.17972614
2.9603-3.72910.21681280.16742654
3.7291-36.050.20611610.16552756

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