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- PDB-4zbe: Crystal structure of KPC-2 beta-lactamase complexed with avibactam -

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Basic information

Entry
Database: PDB / ID: 4zbe
TitleCrystal structure of KPC-2 beta-lactamase complexed with avibactam
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
CITRIC ACID / Chem-NXL / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNguyen, N.Q. / van den Akker, F.
CitationJournal: Plos One / Year: 2015
Title: Inhibition of Klebsiella beta-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study.
Authors: Krishnan, N.P. / Nguyen, N.Q. / Papp-Wallace, K.M. / Bonomo, R.A. / van den Akker, F.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,4523
Polymers27,9931
Non-polymers4592
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint2 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.315, 66.695, 73.208
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 / KPC-2 beta-lactamase


Mass: 27992.506 Da / Num. of mol.: 1 / Fragment: UNP residues 26-289
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: 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 / Comment: antibiotic, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG6000, 100 mM potassium thiocyanate, 100 mM citrate, pH 4.0, crystals soaked for 8 minutes with 5 mM avibactam in mother liquor (25% PEG600, 100 mM citrate, pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1272 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22206 / % possible obs: 93.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.9 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RXW

3rxw


Resolution: 1.8→36.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.156 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21912 1136 5.1 %RANDOM
Rwork0.15247 ---
obs0.15569 21017 92.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 30 256 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022081
X-RAY DIFFRACTIONr_bond_other_d0.0010.021972
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9732841
X-RAY DIFFRACTIONr_angle_other_deg0.9263.0024526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7623.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15715318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.621515
X-RAY DIFFRACTIONr_chiral_restr0.2240.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212405
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02468
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_it2.9982.1121078
X-RAY DIFFRACTIONr_mcbond_other2.9862.111076
X-RAY DIFFRACTIONr_mcangle_it3.4423.1471351
X-RAY DIFFRACTIONr_mcangle_other3.4333.1471351
X-RAY DIFFRACTIONr_scbond_it4.6042.511003
X-RAY DIFFRACTIONr_scbond_other4.6032.5111004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1723.6151491
X-RAY DIFFRACTIONr_long_range_B_refined7.71818.8872539
X-RAY DIFFRACTIONr_long_range_B_other7.51418.1962436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 82 -
Rwork0.263 1372 -
obs--84.19 %

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