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- PDB-8g2r: CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH AVIBACTAM -

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Basic information

Entry
Database: PDB / ID: 8g2r
TitleCRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH AVIBACTAM
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/Antibiotic / Beta-lactamase / inhibitor / antibiotic resistance / HYDROLASE / HYDROLASE-Antibiotic 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/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsAlsenani, T. / van den Akker, F.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Exploring avibactam and relebactam inhibition of Klebsiella pneumoniae carbapenemase D179N variant: role of the Omega loop-held deacylation water.
Authors: Alsenani, T.A. / Viviani, S.L. / Papp-Wallace, K.M. / Bonomo, R.A. / van den Akker, F.
History
DepositionFeb 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,4432
Polymers28,1761
Non-polymers2671
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.454, 66.673, 72.435
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-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium acetate pH 6, 1.25 M ammonium citrate dibasic

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.28→49.06 Å / Num. obs: 60468 / % possible obs: 92.8 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.4
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 3.026 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3133 / CC1/2: 0.361 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OV5

2ov5


Resolution: 1.28→49.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.164 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3007 5 %RANDOM
Rwork0.1674 ---
obs0.1692 57263 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.97 Å2 / Biso mean: 20.609 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.28→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 17 235 2220
Biso mean--28.61 33.19 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132191
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172113
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6523004
X-RAY DIFFRACTIONr_angle_other_deg1.451.584861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71820.917109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59115353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3711518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02518
X-RAY DIFFRACTIONr_rigid_bond_restr8.24531
LS refinement shellResolution: 1.28→1.311 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.383 208 -
Rwork0.387 4371 -
obs--96.26 %

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