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- PDB-7llh: KPC-2 F72Y mutant with acylated imipenem -

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Basic information

Entry
Database: PDB / ID: 7llh
TitleKPC-2 F72Y mutant with acylated 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-IM2 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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

Downloads & links

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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)55,8494
Polymers55,2462
Non-polymers6032
Water2,324129
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9242
Polymers27,6231
Non-polymers3011
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)27,9242
Polymers27,6231
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.609, 37.123, 83.655
Angle α, β, γ (deg.)88.118, 88.375, 85.479
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALchain 'A'AA29 - 571 - 29
12SERSERPROPROchain 'A'AA59 - 25230 - 223
13THRTHRLEULEUchain 'A'AA254 - 290224 - 260
14IM2IM2IM2IM2chain 'A'AC301
21VALVALVALVALchain 'B'BB29 - 571 - 29
22SERSERPROPROchain 'B'BB59 - 25230 - 223
23THRTHRLEULEUchain 'B'BB254 - 290224 - 260
24IM2IM2IM2IM2chain 'B'BD301

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Components

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


Mass: 27623.090 Da / Num. of mol.: 2 / Mutation: F72Y
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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
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: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 2.1→36.99 Å / Num. obs: 23701 / % possible obs: 97.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 27.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02966 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.176 Å / Rmerge(I) obs: 0.127 / Num. unique obs: 2374 / CC1/2: 0.981 / % possible all: 97.14

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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: 2.1→36.99 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.3269 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1216 5.13 %
Rwork0.1822 22475 -
obs0.1842 23691 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 0 129 4059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414012
X-RAY DIFFRACTIONf_angle_d0.83025464
X-RAY DIFFRACTIONf_chiral_restr0.0505620
X-RAY DIFFRACTIONf_plane_restr0.0051710
X-RAY DIFFRACTIONf_dihedral_angle_d12.84892382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.190.24641200.20282509X-RAY DIFFRACTION97.05
2.19-2.280.29021210.20032497X-RAY DIFFRACTION97.4
2.28-2.40.23691510.20712434X-RAY DIFFRACTION97.66
2.4-2.560.22531420.19822492X-RAY DIFFRACTION97.41
2.56-2.750.28421410.19952491X-RAY DIFFRACTION97.95
2.75-3.030.2886970.22122536X-RAY DIFFRACTION98.5
3.03-3.470.25981290.19842560X-RAY DIFFRACTION98.64
3.47-4.370.17171230.15782519X-RAY DIFFRACTION99.06
4.37-36.990.18521920.15212437X-RAY DIFFRACTION98.06
Refinement TLS params.Method: refined / Origin x: 1.14776452166 Å / Origin y: -6.184878823 Å / Origin z: 9.38810665377 Å
111213212223313233
T0.101907772152 Å2-0.000942861386237 Å2-0.0470356518746 Å2-0.159423140336 Å2-0.0451159373833 Å2--0.175046315662 Å2
L0.859329198508 °20.0314107540674 °2-0.498057563497 °2-2.15105936049 °2-0.575346942121 °2--1.58062326605 °2
S0.00515066211103 Å °-0.043973480863 Å °0.0418836375308 Å °0.0288650311884 Å °0.0718204979561 Å °0.0745010930028 Å °0.0379716538656 Å °-0.0378443700951 Å °-0.0666784730105 Å °
Refinement TLS groupSelection details: all

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