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- PDB-7llb: Crystal structure of KPC-2 S70G/T215P mutant with hydrolyzed meropenem -

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Basic information

Entry
Database: PDB / ID: 7llb
TitleCrystal structure of KPC-2 S70G/T215P mutant with hydrolyzed meropenem
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / Carbapenemase / Beta-lactamase / Antibiotic Resistance / Beta-lactam / antibiotics
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-8YL / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFurey, I. / Palzkill, T. / Sankaran, B. / 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
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 beta-lactamase.
Authors: Furey, I.M. / Mehta, S.C. / Sankaran, B. / Hu, L. / Prasad, B.V.V. / Palzkill, T.
#1: Journal: J Med Chem / Year: 2018
Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using Beta-Lactamase Inhibitors and Beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using Beta-Lactamase Inhibitors and Beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.
Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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: Carbapenem-hydrolyzing beta-lactamase KPC
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7204
Polymers55,9172
Non-polymers8032
Water10,088560
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3602
Polymers27,9581
Non-polymers4011
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)28,3602
Polymers27,9581
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.495, 37.292, 82.128
Angle α, β, γ (deg.)91.391, 90.372, 93.789
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: 27958.492 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-8YL / (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid / Meropenem, hydrolyzed form


Mass: 401.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 1.88 Å3/Da / Density % sol: 34.74 %
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: 8.2.2 / Wavelength: 0.999952 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999952 Å / Relative weight: 1
ReflectionResolution: 1.67→37.2 Å / Num. obs: 45834 / % possible obs: 96.66 % / Redundancy: 2.6 % / Biso Wilson estimate: 12.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03083 / Net I/σ(I): 16.27
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.08035 / Num. unique obs: 4381 / CC1/2: 0.986

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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: 1.67→37.2 Å / SU ML: 0.1303 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.2344 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 2312 5.04 %
Rwork0.1708 43519 -
obs0.1719 45831 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.96 Å2
Refinement stepCycle: LAST / Resolution: 1.67→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 54 560 4554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01084080
X-RAY DIFFRACTIONf_angle_d0.92335566
X-RAY DIFFRACTIONf_chiral_restr0.3167632
X-RAY DIFFRACTIONf_plane_restr0.007726
X-RAY DIFFRACTIONf_dihedral_angle_d14.98311448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.70.21551400.18422414X-RAY DIFFRACTION90.86
1.7-1.740.22411350.18382500X-RAY DIFFRACTION94.34
1.74-1.780.23861480.19052512X-RAY DIFFRACTION95.51
1.78-1.830.22681480.18552542X-RAY DIFFRACTION95.59
1.83-1.880.23241400.19212506X-RAY DIFFRACTION96.32
1.88-1.930.21921140.17982572X-RAY DIFFRACTION96.34
1.93-1.990.19691430.17022552X-RAY DIFFRACTION96.63
1.99-2.060.21291130.16632598X-RAY DIFFRACTION96.89
2.06-2.150.17941270.16512561X-RAY DIFFRACTION96.86
2.15-2.240.20111070.17162597X-RAY DIFFRACTION97.16
2.24-2.360.1741230.17012596X-RAY DIFFRACTION97.39
2.36-2.510.19971520.17182565X-RAY DIFFRACTION97.49
2.51-2.70.20081420.17752597X-RAY DIFFRACTION97.86
2.7-2.980.2071250.18572600X-RAY DIFFRACTION98.34
2.98-3.410.18291590.17342617X-RAY DIFFRACTION98.65
3.41-4.290.15041580.14892592X-RAY DIFFRACTION98.89
4.29-37.20.18991380.16232598X-RAY DIFFRACTION98.35

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