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- PDB-7a61: Crystal structure of KPC-2 with hydrolyzed faropenem (ring-open form) -

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Basic information

Entry
Database: PDB / ID: 7a61
TitleCrystal structure of KPC-2 with hydrolyzed faropenem (ring-open form)
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / antibiotic / faropenem / catalysis
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-R0B / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Faropenem reacts with serine and metallo-beta-lactamases to give multiple products.
Authors: Lucic, A. / Hinchliffe, P. / Malla, T.R. / Tooke, C.L. / Brem, J. / Calvopina, K. / Lohans, C.T. / Rabe, P. / McDonough, M.A. / Armistead, T. / Orville, A.M. / Spencer, J. / Schofield, C.J.
History
DepositionAug 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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)31,6638
Polymers30,8061
Non-polymers8587
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-35 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.535, 80.033, 56.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

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Components

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


Mass: 30805.646 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-R0B / (2~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-butyl-2,3-dihydro-1,3-thiazole-4-carboxylic acid / hydrolyzed faropenem (ring-open form)


Mass: 289.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 5% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.89996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89996 Å / Relative weight: 1
ReflectionResolution: 1.25→48.28 Å / Num. obs: 75948 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.046 / Net I/σ(I): 9.2
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3711 / CC1/2: 0.703 / Rpim(I) all: 0.823

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QW9

6qw9


Resolution: 1.25→48.28 Å / SU ML: 0.1387 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1595 3855 5.09 %
Rwork0.1325 71934 -
obs0.1339 75789 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 50 343 2400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792250
X-RAY DIFFRACTIONf_angle_d1.04023081
X-RAY DIFFRACTIONf_chiral_restr0.0753338
X-RAY DIFFRACTIONf_plane_restr0.0073405
X-RAY DIFFRACTIONf_dihedral_angle_d18.3541813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.32711360.32542508X-RAY DIFFRACTION99.47
1.27-1.280.31441300.28622520X-RAY DIFFRACTION99.59
1.28-1.30.29291440.26572512X-RAY DIFFRACTION99.62
1.3-1.320.29221580.26812517X-RAY DIFFRACTION99.7
1.32-1.330.26691400.26342554X-RAY DIFFRACTION99.81
1.33-1.350.27021480.25442540X-RAY DIFFRACTION99.78
1.35-1.380.25391380.2252525X-RAY DIFFRACTION99.85
1.38-1.40.19221430.19612534X-RAY DIFFRACTION99.78
1.4-1.420.18641140.18422552X-RAY DIFFRACTION99.74
1.42-1.450.21321290.15532532X-RAY DIFFRACTION99.63
1.45-1.480.19011350.14672587X-RAY DIFFRACTION99.93
1.48-1.510.16411060.13952545X-RAY DIFFRACTION99.96
1.51-1.540.15961390.13282565X-RAY DIFFRACTION99.96
1.54-1.570.17511440.1232538X-RAY DIFFRACTION99.85
1.57-1.610.14851430.11582549X-RAY DIFFRACTION99.85
1.61-1.660.14691470.10982541X-RAY DIFFRACTION99.81
1.66-1.710.15781400.11162569X-RAY DIFFRACTION100
1.71-1.760.16341300.10482565X-RAY DIFFRACTION100
1.76-1.820.13011220.10762602X-RAY DIFFRACTION100
1.82-1.90.14281230.10892572X-RAY DIFFRACTION100
1.9-1.980.12821510.10622562X-RAY DIFFRACTION99.96
1.98-2.090.13681310.10182615X-RAY DIFFRACTION99.96
2.09-2.220.12751400.10162579X-RAY DIFFRACTION100
2.22-2.390.11691380.10032584X-RAY DIFFRACTION99.96
2.39-2.630.13491300.10552616X-RAY DIFFRACTION99.96
2.63-3.010.13491370.11562626X-RAY DIFFRACTION100
3.01-3.790.141500.12182655X-RAY DIFFRACTION100
3.8-48.280.1681690.14692770X-RAY DIFFRACTION99.93

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