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- PDB-6v1j: Structure of KPC-2 bound to QPX7728 at 1.30 A -

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Basic information

Entry
Database: PDB / ID: 6v1j
TitleStructure of KPC-2 bound to QPX7728 at 1.30 A
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / HYDROLASE / 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-QNA / Chem-RM9 / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201600026C United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases.
Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N.
History
DepositionNov 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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

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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)31,5526
Polymers30,8071
Non-polymers7455
Water5,819323
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)55.660, 59.990, 78.160
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-497-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 328 molecules

#2: Chemical ChemComp-RM9 / (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 221.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8BFO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QNA / (1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 238.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9BFO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.34 Å / Num. obs: 65033 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.99 / Num. measured all: 21968 / Num. unique obs: 3161 / CC1/2: 0.638 / Net I/σ(I) obs: 1.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.46 Å40.8 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.3phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL8

5ul8


Resolution: 1.3→40.8 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1802 6018 4.84 %
Rwork0.1443 --
obs0.146 65014 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.92 Å2 / Biso mean: 16.4974 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 1.3→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 49 323 2388
Biso mean--31.07 34.22 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.3-1.310.32191850.282639324117
1.31-1.330.33772130.273139524165
1.33-1.350.27862000.258539174117
1.35-1.360.24062190.249839564175
1.36-1.380.27792130.231638764089
1.38-1.40.22921750.222839664141
1.4-1.420.26252000.211739534153
1.42-1.440.22741950.200639344129
1.44-1.460.21961810.186139774158
1.46-1.490.2272120.177739414153
1.49-1.510.16672200.164739344154
1.51-1.540.22562200.163539094129
1.54-1.570.18061810.160639624143
1.57-1.60.18351710.140939954166
1.6-1.640.17462020.135939384140
1.64-1.680.15752080.135139264134
1.68-1.720.17532030.129539524155
1.72-1.760.18351830.122339954178
1.76-1.820.17091870.121839504137
1.82-1.870.15531950.118139064101
1.87-1.940.16781960.117939744170
1.94-2.020.15422070.111239274134
2.02-2.110.15251940.112739414135
2.11-2.220.12811930.113640044197
2.22-2.360.16031990.123439314130
2.36-2.540.1762200.132239004120
2.54-2.80.16172640.123739014165
2.8-3.210.17652310.134139064137
3.21-4.040.16521490.127240174166
4.04-40.80.17312020.151439384140

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