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

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Basic information

Entry
Database: PDB / ID: 7lnl
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 / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8YF / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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
CitationJournal: 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.
History
DepositionFeb 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Jul 21, 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 13, 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:
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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
Water10,467581
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.: 581 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
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: 1.82→37.64 Å / Num. obs: 36229 / % possible obs: 96.61 % / Redundancy: 3 % / Biso Wilson estimate: 10.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.91
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 3598 / CC1/2: 0.992

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Processing

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

3c5a


Resolution: 1.82→37.64 Å / SU ML: 0.1624 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 17.6054 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 1764 4.87 %
Rwork0.1525 34464 -
obs0.1541 36228 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.09 Å2
Refinement stepCycle: LAST / Resolution: 1.82→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 42 581 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994066
X-RAY DIFFRACTIONf_angle_d0.96775540
X-RAY DIFFRACTIONf_chiral_restr0.0789626
X-RAY DIFFRACTIONf_plane_restr0.0063726
X-RAY DIFFRACTIONf_dihedral_angle_d17.70611452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.22441300.17812650X-RAY DIFFRACTION96.16
1.87-1.920.23091230.16522651X-RAY DIFFRACTION96.39
1.92-1.990.19691450.16322653X-RAY DIFFRACTION96.52
1.99-2.060.20421550.15052597X-RAY DIFFRACTION96.73
2.06-2.140.20111710.15222641X-RAY DIFFRACTION96.97
2.14-2.240.17981510.14552657X-RAY DIFFRACTION97.13
2.24-2.350.18511340.15352690X-RAY DIFFRACTION97.41
2.35-2.50.17311190.15142704X-RAY DIFFRACTION97.75
2.5-2.70.20681340.15282677X-RAY DIFFRACTION97.91
2.7-2.970.1781050.15822703X-RAY DIFFRACTION98.15
2.97-3.40.19131360.15512712X-RAY DIFFRACTION98.51
3.4-4.280.15751230.13232703X-RAY DIFFRACTION97.31
4.28-37.640.17251380.15882426X-RAY DIFFRACTION89.21
Refinement TLS params.Method: refined / Origin x: -18.3738042443 Å / Origin y: -5.59641620804 Å / Origin z: -8.4804609381 Å
111213212223313233
T0.0143063397191 Å20.00711348610182 Å20.000268119023134 Å2-0.0124359493108 Å20.00249186174382 Å2--0.0197866477152 Å2
L0.074241741856 °20.0292644586294 °2-0.0122339058977 °2-0.0415770274622 °2-0.0122976229321 °2--0.0448127652098 °2
S0.0168586356409 Å °0.0106259627468 Å °0.00701161533502 Å °0.00532337895003 Å °-0.0044587028754 Å °-0.0101677654178 Å °0.00809362812283 Å °0.00793716931619 Å °0.00712262274478 Å °
Refinement TLS groupSelection details: all

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