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- PDB-8tjm: Crystal structure of KPC-44 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 8tjm
TitleCrystal structure of KPC-44 carbapenemase
Componentsbeta-lactamase
KeywordsHYDROLASE / KPC carbapenemase / ceftazidime-avibactam resistance
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / response to antibiotic / beta-lactamase
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 23, 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 1.2Oct 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: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6068
Polymers30,0361
Non-polymers5707
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.180, 72.180, 84.981
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-672-

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
Details: ceftazidime-avibactam-resistant / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC / Plasmid: pET28a-TEV
Details (production host): TEV cleavage site between N terminal His tag and the protein of interest
Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: A0A4Y5JTU1, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.19 %
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 / Ambient temp details: room termperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00002 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.28→33.22 Å / Num. obs: 66426 / % possible obs: 97.44 % / Redundancy: 11.7 % / Biso Wilson estimate: 13.82 Å2 / CC1/2: 0.969 / Net I/σ(I): 14
Reflection shellResolution: 1.28→1.33 Å / Num. unique obs: 4939 / CC1/2: 0.835 / % possible all: 75.34

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
iMOSFLM7.3.0data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→33.22 Å / SU ML: 0.1048 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1666 3270 5.06 %
Rwork0.1451 61399 -
obs0.1462 64669 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.57 Å2
Refinement stepCycle: LAST / Resolution: 1.28→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 32 172 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522100
X-RAY DIFFRACTIONf_angle_d0.9092870
X-RAY DIFFRACTIONf_chiral_restr0.0807328
X-RAY DIFFRACTIONf_plane_restr0.0089371
X-RAY DIFFRACTIONf_dihedral_angle_d5.8256307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.2703690.22521466X-RAY DIFFRACTION53.9
1.3-1.320.24731180.19762434X-RAY DIFFRACTION89.95
1.32-1.340.22491550.17312661X-RAY DIFFRACTION98.74
1.34-1.360.211300.15572735X-RAY DIFFRACTION100
1.36-1.390.19821300.14622742X-RAY DIFFRACTION100
1.39-1.420.18081430.1412696X-RAY DIFFRACTION100
1.42-1.440.15971370.13682723X-RAY DIFFRACTION99.97
1.44-1.480.15081450.13482699X-RAY DIFFRACTION100
1.48-1.510.17341400.13532741X-RAY DIFFRACTION100
1.51-1.550.19731330.12142720X-RAY DIFFRACTION100
1.55-1.590.13851450.11922724X-RAY DIFFRACTION99.93
1.59-1.640.15251550.11142711X-RAY DIFFRACTION99.97
1.64-1.690.15551470.11422736X-RAY DIFFRACTION100
1.69-1.750.14561650.12092683X-RAY DIFFRACTION99.96
1.75-1.820.14271700.122716X-RAY DIFFRACTION99.9
1.82-1.90.14271480.12672731X-RAY DIFFRACTION99.93
1.9-20.15171660.12452725X-RAY DIFFRACTION100
2-2.130.16191440.12482755X-RAY DIFFRACTION100
2.13-2.290.14431370.132753X-RAY DIFFRACTION100
2.29-2.520.15611440.14932762X-RAY DIFFRACTION99.97
2.52-2.890.15841580.15492784X-RAY DIFFRACTION100
2.89-3.640.18251660.16162791X-RAY DIFFRACTION100
3.64-33.220.18271250.16692911X-RAY DIFFRACTION98.38

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