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- PDB-7ljk: Crystal structure of the deacylation deficient KPC-2 F72Y mutant -

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Basic information

Entry
Database: PDB / ID: 7ljk
TitleCrystal structure of the deacylation deficient KPC-2 F72Y mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / KPC / Carbapenemase / Beta-lactamase / Antibiotic Resistance / Enzyme / Beta-lactam / antibiotics
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionJan 29, 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.id ..._citation.country / _citation.id / _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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)56,0172
Polymers56,0172
Non-polymers00
Water7,098394
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0091
Polymers28,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0091
Polymers28,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.325, 37.310, 82.178
Angle α, β, γ (deg.)92.430, 90.413, 94.617
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 Beta-lactamase


Mass: 28008.506 Da / Num. of mol.: 2 / Mutation: F72Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_ ...Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_27040, DN589_26110, EAO17_31575, FKC87_27985, GF489_24625, GS419_28405, IPF_358, KP64477d_00006, KPC_069, p628KPC_020, pCRE79_15, pCT-KPC_129, pFOS18_014, pkp469IL_0095, pkp53il_00095, SAMEA3649709_04840, SAMEA3649772_05181, UC330_005, UC332_005, UC334_005
Production host: Escherichia coli (E. coli) / References: UniProt: Q93LQ9, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
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: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.81→37.15 Å / Num. obs: 32888 / % possible obs: 88.88 % / Redundancy: 1.8 % / Biso Wilson estimate: 6.99 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.05725 / Net I/σ(I): 10.84
Reflection shellResolution: 1.81→1.875 Å / Num. unique obs: 3244 / CC1/2: 0.8763

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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: 1.81→37.15 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.4234 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1599 4.86 %
Rwork0.1567 31283 -
obs0.1586 32882 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.75 Å2
Refinement stepCycle: LAST / Resolution: 1.81→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 394 4330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714018
X-RAY DIFFRACTIONf_angle_d0.90315476
X-RAY DIFFRACTIONf_chiral_restr0.0572624
X-RAY DIFFRACTIONf_plane_restr0.0067714
X-RAY DIFFRACTIONf_dihedral_angle_d3.03062390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.870.20411550.14582789X-RAY DIFFRACTION87.85
1.87-1.940.21530.15352770X-RAY DIFFRACTION86.66
1.94-2.010.18881420.15522795X-RAY DIFFRACTION87.44
2.01-2.10.20981430.15872854X-RAY DIFFRACTION89.41
2.1-2.220.2151310.15452872X-RAY DIFFRACTION89.27
2.22-2.350.23071260.1542878X-RAY DIFFRACTION89.17
2.35-2.540.17961400.15442835X-RAY DIFFRACTION88.33
2.54-2.790.19471220.15782851X-RAY DIFFRACTION88.56
2.79-3.190.1931430.16182822X-RAY DIFFRACTION88.56
3.19-4.020.16781480.15613010X-RAY DIFFRACTION93.35
4.02-37.150.21031960.16162807X-RAY DIFFRACTION89.24
Refinement TLS params.Method: refined / Origin x: 16.5512149977 Å / Origin y: 13.6164919473 Å / Origin z: 8.93250055521 Å
111213212223313233
T0.00249997392642 Å20.010596463347 Å20.0219221783564 Å2-0.0311820394859 Å20.00785163919 Å2--0.0295471804217 Å2
L0.265229424011 °20.14213175909 °20.247089711054 °2-0.30949282892 °20.185717698157 °2--0.36697320723 °2
S0.000305422929084 Å °0.016488324391 Å °0.00279712896233 Å °0.0267030734765 Å °-0.00244435007744 Å °0.0080672968123 Å °-0.00915837642323 Å °0.0215165156885 Å °-0.00165960553335 Å °
Refinement TLS groupSelection details: all

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