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- PDB-7tc1: Crystal structure of D179N KPC-2 beta-lactamase in complex with v... -

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Basic information

Entry
Database: PDB / ID: 7tc1
TitleCrystal structure of D179N KPC-2 beta-lactamase in complex with vaborbactam
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Vaborbactam / PHOSPHATE ION / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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 22, 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
Revision 1.4Oct 23, 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5683
Polymers28,1761
Non-polymers3922
Water6,738374
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)51.209, 66.021, 72.950
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-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M Sodium citrate HCl pH 4, 0.8 M Ammonium sulfate

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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: 0.97935 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.16→27.76 Å / Num. obs: 83367 / % possible obs: 98.8 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.2
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5359 / CC1/2: 0.88 / % possible all: 84.2

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Processing

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

2ov5


Resolution: 1.16→27.76 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.975 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1576 4171 4.9 %RANDOM
Rwork0.1274 ---
obs0.1289 80550 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.4 Å2 / Biso mean: 12.372 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.16→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 30 375 2382
Biso mean--14.01 27.94 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132125
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171975
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.6462906
X-RAY DIFFRACTIONr_angle_other_deg1.71.5724572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47821.346104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35815328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_rigid_bond_restr4.31534100
LS refinement shellResolution: 1.161→1.191 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 244 -
Rwork0.183 4870 -
all-5114 -
obs--81.77 %

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