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- PDB-6m7i: Crystal structure of KPC-2 with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6m7i
TitleCrystal structure of KPC-2 with compound 3
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/INHIBITOR / Carbapenemase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-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-J84 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 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)AI103158 United States
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
Authors: Torelli, N.J. / Akhtar, A. / DeFrees, K. / Jaishankar, P. / Pemberton, O.A. / Zhang, X. / Johnson, C. / Renslo, A.R. / Chen, Y.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,0836
Polymers30,8071
Non-polymers1,2775
Water2,882160
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)56.743, 59.244, 76.277
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-449-

HOH

21A-560-

HOH

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Components

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


Mass: 30806.631 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-J84 / 1-(2,4-dichlorophenyl)-4-(1H-tetrazol-5-yl)-1H-pyrazol-5-amine


Mass: 296.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7Cl2N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.89 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28898 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Χ2: 1.724 / Net I/σ(I): 16.8 / Num. measured all: 201534
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.735.40.43612950.9350.2060.4831.38990.8
1.73-1.7660.39214190.950.1740.4291.465100
1.76-1.796.40.31814290.970.1370.3471.489100
1.79-1.8370.28514450.9790.1160.3081.507100
1.83-1.877.30.24514060.9840.0980.2641.575100
1.87-1.917.20.20314320.990.0810.2191.635100
1.91-1.967.30.16214350.9920.0640.1741.732100
1.96-2.027.30.13914390.9940.0550.151.684100
2.02-2.077.20.11314350.9960.0450.1221.783100
2.07-2.147.30.09514250.9970.0380.1031.721100
2.14-2.227.30.0814380.9970.0320.0861.718100
2.22-2.317.20.07214510.9980.0290.0781.803100
2.31-2.417.30.06314500.9980.0250.0681.711100
2.41-2.547.30.05314440.9990.0210.0571.675100
2.54-2.77.20.04914580.9990.0190.0521.801100
2.7-2.917.20.04314500.9990.0170.0471.78100
2.91-3.27.10.03814890.9990.0150.0411.837100
3.2-3.667.10.03314690.9990.0130.0361.90699.9
3.66-4.616.90.03115080.9990.0130.0331.878100
4.61-506.40.03515810.9990.0150.0382.18198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.39 Å31.65 Å
Translation6.39 Å31.65 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.701→31.653 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2104 1987 6.89 %
Rwork0.1787 --
obs0.1809 28849 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.09 Å2 / Biso mean: 27.71 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 1.701→31.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 82 160 2236
Biso mean--38.73 37.14 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.701-1.74360.28091460.22771842198898
1.7436-1.79070.25381280.222518942022100
1.7907-1.84340.27371480.212318852033100
1.8434-1.90290.22921420.201719142056100
1.9029-1.97090.21821410.189518892030100
1.9709-2.04980.271390.184818882027100
2.0498-2.14310.23071370.179219002037100
2.1431-2.2560.21551400.18619142054100
2.256-2.39730.22881430.192719052048100
2.3973-2.58240.20971420.176419352077100
2.5824-2.84210.20581420.175119302072100
2.8421-3.2530.20211460.18819272073100
3.253-4.0970.1771470.15719732120100
4.097-31.65860.20051460.16932066221299

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