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- PDB-8tmr: Crystal structure of KPC-44 carbapenemase complexed with avibactam -

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Basic information

Entry
Database: PDB / ID: 8tmr
TitleCrystal structure of KPC-44 carbapenemase complexed with avibactam
Componentsbeta-lactamase
KeywordsHYDROLASE / KPC carbapenemase / ceftazidime-avibactam 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
Chem-NXL / PHOSPHATE ION / beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsSun, Z. / Palzkill, T. / Hu, L. / Lin, H. / Sankaran, B. / Wang, J. / Prasad, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops.
Authors: Sun, Z. / Lin, H. / Hu, L. / Neetu, N. / Sankaran, B. / Wang, J. / Prasad, B.V.V. / Palzkill, T.
History
DepositionJul 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 13, 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: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5225
Polymers30,0361
Non-polymers4864
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.760, 71.760, 84.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-2266-

HOH

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Components

#1: Protein beta-lactamase


Mass: 30035.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: A0A4Y5JTU1, 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.0-4.4, and 22-24% (w/v) PEG 1000
PH range: 4.0 - 4.4 / Temp details: 25oC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999983 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999983 Å / Relative weight: 1
ReflectionResolution: 1.37→42.29 Å / Num. obs: 53437 / % possible obs: 99.89 % / Redundancy: 12.08 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 21.09
Reflection shellResolution: 1.37→1.42 Å / Mean I/σ(I) obs: 5.86 / Num. unique obs: 5271 / CC1/2: 0.96 / CC star: 0.99 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→34.96 Å / SU ML: 0.1022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.5209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1624 2721 5.1 %
Rwork0.1346 50622 -
obs0.136 53343 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.87 Å2
Refinement stepCycle: LAST / Resolution: 1.37→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 30 268 2260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542032
X-RAY DIFFRACTIONf_angle_d0.96972765
X-RAY DIFFRACTIONf_chiral_restr0.0833313
X-RAY DIFFRACTIONf_plane_restr0.013358
X-RAY DIFFRACTIONf_dihedral_angle_d7.2341299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.18221540.14572610X-RAY DIFFRACTION100
1.4-1.420.16491630.12652635X-RAY DIFFRACTION100
1.42-1.450.16581400.122600X-RAY DIFFRACTION100
1.45-1.480.15881340.11522649X-RAY DIFFRACTION99.96
1.48-1.520.1252950.11212710X-RAY DIFFRACTION100
1.52-1.550.16711260.11592651X-RAY DIFFRACTION100
1.55-1.60.1481310.10932658X-RAY DIFFRACTION100
1.6-1.640.14361390.10692618X-RAY DIFFRACTION99.96
1.64-1.70.17261490.11472645X-RAY DIFFRACTION100
1.7-1.760.15281510.11292652X-RAY DIFFRACTION100
1.76-1.830.14981550.11592637X-RAY DIFFRACTION100
1.83-1.910.14421280.12472680X-RAY DIFFRACTION99.96
1.91-2.010.14961400.12642658X-RAY DIFFRACTION100
2.01-2.140.1591570.12542661X-RAY DIFFRACTION100
2.14-2.30.16621490.13142661X-RAY DIFFRACTION100
2.3-2.530.17491500.14342695X-RAY DIFFRACTION100
2.53-2.90.17721330.14942692X-RAY DIFFRACTION100
2.9-3.650.1491670.1472718X-RAY DIFFRACTION100
3.66-34.960.17571600.15142792X-RAY DIFFRACTION98.47

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