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- PDB-8tn0: Crystal structure of KPC-44 carbapenemase w/o cryoprotectant -

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Basic information

Entry
Database: PDB / ID: 8tn0
TitleCrystal structure of KPC-44 carbapenemase w/o cryoprotectant
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: 1.31 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 31, 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)30,2283
Polymers30,0361
Non-polymers1922
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.338, 72.338, 84.715
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-827-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 42.24 %
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: 1.31→35 Å / Num. obs: 61867 / % possible obs: 97.18 % / Redundancy: 10.3 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 0.952 / Rpim(I) all: 0.017 / Rrim(I) all: 0.055 / Net I/σ(I): 15.1
Reflection shellResolution: 1.31→1.36 Å / Num. unique obs: 4503 / CC1/2: 0.736 / % possible all: 73.57

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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: 1.31→33.26 Å / SU ML: 0.1098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.2469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1616 3048 5.07 %
Rwork0.1358 57045 -
obs0.1371 60093 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.99 Å2
Refinement stepCycle: LAST / Resolution: 1.31→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 10 332 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532003
X-RAY DIFFRACTIONf_angle_d0.90782731
X-RAY DIFFRACTIONf_chiral_restr0.0779308
X-RAY DIFFRACTIONf_plane_restr0.0102357
X-RAY DIFFRACTIONf_dihedral_angle_d5.5968286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.2584720.24071446X-RAY DIFFRACTION54.82
1.33-1.350.25341070.20952302X-RAY DIFFRACTION87.44
1.35-1.380.22021240.1722630X-RAY DIFFRACTION98.25
1.38-1.40.211440.15952612X-RAY DIFFRACTION99.96
1.4-1.430.17381420.14282640X-RAY DIFFRACTION100
1.43-1.460.18221380.13822647X-RAY DIFFRACTION100
1.46-1.490.18221400.13232613X-RAY DIFFRACTION100
1.49-1.520.15471330.13092694X-RAY DIFFRACTION100
1.52-1.560.17811480.12852632X-RAY DIFFRACTION99.96
1.56-1.60.13651360.11462660X-RAY DIFFRACTION100
1.61-1.650.17221230.11582652X-RAY DIFFRACTION100
1.65-1.710.14631380.11492654X-RAY DIFFRACTION100
1.71-1.770.14561690.1212651X-RAY DIFFRACTION100
1.77-1.840.16331590.12152620X-RAY DIFFRACTION100
1.84-1.920.14041480.13112685X-RAY DIFFRACTION99.93
1.92-2.020.16771350.11722674X-RAY DIFFRACTION100
2.02-2.150.13941620.12592641X-RAY DIFFRACTION100
2.15-2.310.14591230.12162701X-RAY DIFFRACTION100
2.31-2.550.16691520.14222680X-RAY DIFFRACTION100
2.55-2.920.15911420.14092726X-RAY DIFFRACTION99.97
2.92-3.670.17151630.13842720X-RAY DIFFRACTION100
3.67-33.260.15581500.14722765X-RAY DIFFRACTION97.3

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