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- PDB-7tb7: Crystal structure of D179N KPC-2 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 7tb7
TitleCrystal structure of D179N KPC-2 beta-lactamase
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance
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/transpeptidase-like
Similarity search - Domain/homology
CITRIC ACID / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
Authorsvan den Akker, F. / Alsenani, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142049 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2022
Title: Structural Characterization of the D179N and D179Y Variants of KPC-2 beta-Lactamase: Omega-Loop Destabilization as a Mechanism of Resistance to Ceftazidime-Avibactam.
Authors: Alsenani, T.A. / Viviani, S.L. / Kumar, V. / Taracila, M.A. / Bethel, C.R. / Barnes, M.D. / Papp-Wallace, K.M. / Shields, R.K. / Nguyen, M.H. / Clancy, C.J. / Bonomo, R.A. / van den Akker, F.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 4, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3682
Polymers28,1761
Non-polymers1921
Water5,981332
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)51.040, 66.251, 72.441
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: 28175.754 Da / Num. of mol.: 1 / Mutation: D179N
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 6000, 100 mM citrate pH 4.0, and 100 mM KSCN, 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 EIGER2 X 9M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 0.99→27.79 Å / Num. obs: 120566 / % possible obs: 87.2 % / Redundancy: 10.6 % / Biso Wilson estimate: 8.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Net I/σ(I): 39.3
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1705 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OV5

2ov5


Resolution: 0.99→27.79 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1443 5960 4.95 %
Rwork0.1285 114485 -
obs0.1293 120445 87.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.13 Å2 / Biso mean: 12.4141 Å2 / Biso min: 6.1 Å2
Refinement stepCycle: final / Resolution: 0.99→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 13 332 2317
Biso mean--10.94 23.84 -
Num. residues----264
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.99-10.2709140.24623543688
1-1.010.2449440.2095957100122
1.01-1.020.2103860.18311596168236
1.02-1.040.15741120.15972167227950
1.04-1.050.17381650.13552677284263
1.05-1.060.15231550.12693127328272
1.06-1.080.14791800.10883478365880
1.08-1.090.12142030.10253841404489
1.09-1.110.12452170.09224081429894
1.11-1.130.11292220.08534227444997
1.13-1.150.11551850.08584334451999
1.15-1.170.09692270.088443684595100
1.17-1.190.09992290.087343494578100
1.19-1.220.11152140.093843614575100
1.22-1.240.12422320.096343694601100
1.24-1.270.11252340.100243244558100
1.27-1.30.13452120.101243844596100
1.3-1.340.12172330.108943424575100
1.34-1.380.13112240.10543814605100
1.38-1.420.11542480.103143694617100
1.42-1.470.11792160.100443624578100
1.47-1.530.11842290.101843844613100
1.53-1.60.12242410.106343794620100
1.6-1.690.13352190.117743934612100
1.69-1.790.13582500.13243854635100
1.79-1.930.1432610.133243784639100
1.93-2.130.14282280.134244654693100
2.13-2.430.15482270.143644444671100
2.43-3.060.16122220.159945294751100
3.07-27.790.18792310.155946804911100

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