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- PDB-8g2t: CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELE... -

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Basic information

Entry
Database: PDB / ID: 8g2t
TitleCRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELEBACTAM (IMINE HYDROLYSIS INTERMEDIATE)
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/Inhibitor / Beta-lactamase / inhibitor / antibiotic resistance / 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
PHOSPHATE ION / Chem-YOZ / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 1.3Nov 20, 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)28,5413
Polymers28,1761
Non-polymers3652
Water6,774376
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)50.795, 66.227, 72.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-YOZ / (2S,5R)-5-amino-1-formyl-5-hydroxy-N-(piperidin-4-yl)piperidine-2-carboxamide / Relebactam, the acylated, desulfated, imine-hydrolysis intermediate


Mass: 270.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O3 / 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.: 376 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM HEPES pH 8.0 and 0.8 M NaH2PO4, 0.8 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 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: 1.26→29.63 Å / Num. obs: 66874 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4781 / CC1/2: 0.931 / % possible all: 98.4

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Processing

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

2ov5


Resolution: 1.26→27.76 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.598 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16746 3309 5 %RANDOM
Rwork0.13372 ---
obs0.13538 63495 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.07 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.26→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 24 376 2365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171950
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6442842
X-RAY DIFFRACTIONr_angle_other_deg1.5131.5744507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10921.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7431515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6281.3141067
X-RAY DIFFRACTIONr_mcbond_other4.6311.3121065
X-RAY DIFFRACTIONr_mcangle_it6.8831.9691334
X-RAY DIFFRACTIONr_mcangle_other6.8821.9681334
X-RAY DIFFRACTIONr_scbond_it2.5441.4731011
X-RAY DIFFRACTIONr_scbond_other2.5461.4741008
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0892.1371499
X-RAY DIFFRACTIONr_long_range_B_refined6.23117.8882539
X-RAY DIFFRACTIONr_long_range_B_other6.01216.4572423
X-RAY DIFFRACTIONr_rigid_bond_restr4.97534028
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.262→1.294 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 232 -
Rwork0.153 4544 -
obs--98.45 %

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