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- PDB-8tmt: Crystal structure of KPC-44 carbapenemase in complex with vaborbactam -

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Basic information

Entry
Database: PDB / ID: 8tmt
TitleCrystal structure of KPC-44 carbapenemase in complex with vaborbactam
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
Vaborbactam / : / beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSun, Z. / Palzkill, T. / Hu, L. / Neetu, N. / Lin, H. / Sankaran, B. / Wang, J. / Prasad, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
Welch FoundationQ1279 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 6, 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)30,7329
Polymers30,0361
Non-polymers6968
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.380, 72.380, 85.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
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-1110-

HOH

21A-1202-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 7 types, 310 molecules

#2: Chemical ChemComp-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.96 %
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: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.7→50.553 Å / Num. obs: 29050 / % possible obs: 100 % / Redundancy: 10.58 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 5 / Num. unique obs: 4184 / CC1/2: 0.926 / Rpim(I) all: 0.154 / Rrim(I) all: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLM7.3.0data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.553 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 1513 5.21 %
Rwork0.1606 --
obs0.1627 29016 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→50.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 43 302 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172016
X-RAY DIFFRACTIONf_angle_d1.4842756
X-RAY DIFFRACTIONf_dihedral_angle_d3.4861582
X-RAY DIFFRACTIONf_chiral_restr0.101314
X-RAY DIFFRACTIONf_plane_restr0.01358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75490.23981250.20812470X-RAY DIFFRACTION100
1.7549-1.81760.25381120.18942496X-RAY DIFFRACTION100
1.8176-1.89040.21451450.16862465X-RAY DIFFRACTION100
1.8904-1.97640.2491580.16612443X-RAY DIFFRACTION100
1.9764-2.08060.19961400.15862482X-RAY DIFFRACTION100
2.0806-2.2110.20261270.15292482X-RAY DIFFRACTION100
2.211-2.38170.20981500.15412475X-RAY DIFFRACTION100
2.3817-2.62140.21161430.16022502X-RAY DIFFRACTION100
2.6214-3.00060.20321200.16512512X-RAY DIFFRACTION100
3.0006-3.78030.1821260.15322553X-RAY DIFFRACTION100
3.7803-50.5530.18461670.15652623X-RAY DIFFRACTION100

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