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- PDB-7lr9: Crystal structure of KPC-2 S70G/T215P mutant with hydrolyzed imipenem -

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Basic information

Entry
Database: PDB / ID: 7lr9
TitleCrystal structure of KPC-2 S70G/T215P mutant with hydrolyzed imipenem
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/ANTIBIOTIC / KPC / Carbapenemase / Beta-lactamase / Hydrolase / Antibiotic Resistance / Enzyme / Beta-lactam / antibiotics / HYDROLASE-ANTIBIOTIC complex
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-8YF / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsFurey, I. / Palzkill, T. / Hu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: To Be Published
Title: Crystal structure of KPC-2 T215P mutant
Authors: Furey, I.M. / Palzkill, T.
History
DepositionFeb 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2654
Polymers56,6302
Non-polymers6352
Water10,719595
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3151
Non-polymers3171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3151
Non-polymers3171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.673, 37.743, 82.706
Angle α, β, γ (deg.)91.543, 90.372, 93.844
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 28314.910 Da / Num. of mol.: 2 / Mutation: S70G, T215P
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-8YF / (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid / Imipenem, hydrolyzed form


Mass: 317.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 8,000, 0.1M KsCN, 0.1M Sodium Acetate pH:4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.47→37.64 Å / Num. obs: 68235 / % possible obs: 95.86 % / Redundancy: 3 % / Biso Wilson estimate: 10.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04879 / Net I/σ(I): 12.4
Reflection shellResolution: 1.47→1.523 Å / Rmerge(I) obs: 0.101 / Num. unique obs: 6730 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.47→37.64 Å / SU ML: 0.1218 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 17.6412 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1806 3369 4.94 %
Rwork0.1705 64864 -
obs0.171 68233 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.15 Å2
Refinement stepCycle: LAST / Resolution: 1.47→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 42 595 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00654066
X-RAY DIFFRACTIONf_angle_d0.95125540
X-RAY DIFFRACTIONf_chiral_restr0.0789626
X-RAY DIFFRACTIONf_plane_restr0.006726
X-RAY DIFFRACTIONf_dihedral_angle_d17.69061452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.22761520.17482632X-RAY DIFFRACTION94.25
1.49-1.510.20951550.18242681X-RAY DIFFRACTION94.25
1.51-1.540.20361310.17812605X-RAY DIFFRACTION94.21
1.54-1.560.18231260.1742706X-RAY DIFFRACTION94.78
1.56-1.590.2281660.17932680X-RAY DIFFRACTION94.65
1.59-1.620.20361650.17562590X-RAY DIFFRACTION94.9
1.62-1.650.19631630.16582754X-RAY DIFFRACTION95.3
1.65-1.680.1991210.16942595X-RAY DIFFRACTION95.13
1.68-1.720.1771210.17652785X-RAY DIFFRACTION95.66
1.72-1.760.18071350.17062682X-RAY DIFFRACTION95.82
1.76-1.80.2231340.18082735X-RAY DIFFRACTION95.82
1.8-1.850.19181150.17962691X-RAY DIFFRACTION96.16
1.85-1.910.20841340.17822747X-RAY DIFFRACTION96.23
1.91-1.970.17911420.17752706X-RAY DIFFRACTION96.48
1.97-2.040.19121640.1662745X-RAY DIFFRACTION97
2.04-2.120.18791630.16292673X-RAY DIFFRACTION96.5
2.12-2.220.18311640.16362723X-RAY DIFFRACTION97.04
2.22-2.330.15841390.16762742X-RAY DIFFRACTION97.46
2.33-2.480.15951240.172788X-RAY DIFFRACTION97.78
2.48-2.670.18851310.17032753X-RAY DIFFRACTION97.8
2.67-2.940.17851170.1792803X-RAY DIFFRACTION98.18
2.94-3.360.16341380.17892765X-RAY DIFFRACTION98.47
3.36-4.240.15431290.1512769X-RAY DIFFRACTION97.44
4.24-37.640.17181400.17182514X-RAY DIFFRACTION89.45

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