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- PDB-7utb: KPC-2 CARBAPENEMASE IN COMPLEX WITH THE BORONIC ACID INHIBITOR MB_076 -

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Basic information

Entry
Database: PDB / ID: 7utb
TitleKPC-2 CARBAPENEMASE IN COMPLEX WITH THE BORONIC ACID INHIBITOR MB_076
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / inhibitor complex / 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-OC0 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
Authorsvan den Akker, F. / Alsenani, T.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M beta-Lactamases: Biochemical and Structural Analyses.
Authors: Alsenani, T.A. / Rodriguez, M.M. / Ghiglione, B. / Taracila, M.A. / Mojica, M.F. / Rojas, L.J. / Hujer, A.M. / Gutkind, G. / Bethel, C.R. / Rather, P.N. / Introvigne, M.L. / Prati, F. / ...Authors: Alsenani, T.A. / Rodriguez, M.M. / Ghiglione, B. / Taracila, M.A. / Mojica, M.F. / Rojas, L.J. / Hujer, A.M. / Gutkind, G. / Bethel, C.R. / Rather, P.N. / Introvigne, M.L. / Prati, F. / Caselli, E. / Power, P. / van den Akker, F. / Bonomo, R.A.
History
DepositionApr 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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)28,5672
Polymers28,1771
Non-polymers3901
Water5,441302
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)51.716, 66.673, 73.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28176.742 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 (E. coli) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-OC0 / [(1~{R})-1-[2-[(5-azanyl-1,3,4-thiadiazol-2-yl)sulfanyl]ethanoylamino]-2-(4-carboxy-1,2,3-triazol-1-yl)ethyl]-$l^{3}-oxidanyl-bis(oxidanyl)boron


Mass: 390.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13BN7O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM citric acid pH 5.5, 100 mM KSCN, 30 % PEG 6K and 10 mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.38→28.04 Å / Num. obs: 52526 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5
Reflection shellResolution: 1.38→1.42 Å / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3670 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OV5

2ov5


Resolution: 1.38→28.04 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.86 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 2688 5.1 %RANDOM
Rwork0.1477 ---
obs0.1489 49772 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.57 Å2 / Biso mean: 14.161 Å2 / Biso min: 7.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.38→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 24 302 2287
Biso mean--21.49 27.38 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171954
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6422868
X-RAY DIFFRACTIONr_angle_other_deg1.6211.5734526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81321.584101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8415326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0461515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 216 -
Rwork0.231 3448 -
all-3664 -
obs--94.95 %

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