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- PDB-7u8s: Crystal Structure of KPC-2 with compound 2 -

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Basic information

Entry
Database: PDB / ID: 7u8s
TitleCrystal Structure of KPC-2 with compound 2
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE inhibitor / beta-lactamase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-LW0 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 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 1.2Oct 30, 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)28,4152
Polymers28,0921
Non-polymers3231
Water2,666148
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)56.060, 59.950, 77.660
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-452-

HOH

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Components

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


Mass: 28091.635 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-LW0 / 3-fluoro-N-[(1R,3S)-3-(1H-tetrazol-5-yl)-2,3-dihydro-1H-inden-1-yl]benzamide


Mass: 323.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14FN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
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: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→59.95 Å / Num. all: 35113 / Num. obs: 35113 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.127 / Rsym value: 0.115 / Net I/av σ(I): 2.8 / Net I/σ(I): 7.9 / Num. measured all: 202758
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.696.10.5261.43096250820.2310.5760.5262.8100
1.69-1.795.70.3821.92735647630.1730.420.3823.599.6
1.79-1.915.10.2552.82263444760.1230.2850.2554.599.1
1.91-2.076.30.17242656442160.0740.1870.1727.399.9
2.07-2.2660.135.22337938840.0570.1430.139.199.8
2.26-2.535.60.1095.81975135220.050.1210.10910.499.6
2.53-2.925.40.08571689831140.0390.0940.08511.999
2.92-3.586.30.0776.91713327020.0330.0840.07714.6100
3.58-5.065.30.15.61116221020.0470.1110.114.599.7
5.06-59.955.50.1363.9691912520.0610.1490.13614.599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.64 Å47.46 Å
Translation5.64 Å47.46 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALA3.3.22data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.6→47.46 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 2001 5.71 %
Rwork0.201 33064 -
obs0.2027 35065 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.07 Å2 / Biso mean: 25.602 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 1.6→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 24 148 2111
Biso mean--41.34 33.01 -
Num. residues----260
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 (%)
1.6-1.640.28351410.262723342475100
1.64-1.680.2891420.253423482490100
1.68-1.730.30571390.240123032442100
1.73-1.790.27921340.22352335246999
1.79-1.850.27111500.22022324247499
1.85-1.930.25011350.20562318245399
1.93-2.020.23231450.204223342479100
2.02-2.120.20091360.197623482484100
2.12-2.260.23731420.193723612503100
2.26-2.430.24941450.207923642509100
2.43-2.670.24261420.19882339248198
2.67-3.060.24941480.202723852533100
3.06-3.850.21281440.190124322576100
3.86-47.460.19941580.187725392697100

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