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- PDB-5uj4: Crystal structure of the KPC-2 beta-lactamase complexed with hydr... -

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Basic information

Entry
Database: PDB / ID: 5uj4
TitleCrystal structure of the KPC-2 beta-lactamase complexed with hydrolyzed faropenem
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/ANTIBIOTIC / carbapenemase / faropenem / beta-lactamase / complex / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SFR / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)4R01AI103158-04 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2).
Authors: Pemberton, O.A. / Zhang, X. / Chen, Y.
History
DepositionJan 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2023
Polymers30,8071
Non-polymers3952
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint1 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.140, 59.130, 77.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

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


Mass: 30806.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-SFR / (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM, unbound, hydrolyzed form


Mass: 303.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO6S / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→46.98 Å / Num. all: 52337 / Num. obs: 52337 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Rsym value: 0.095 / Net I/σ(I): 9.9 / Num. measured all: 367121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.486.60.8884994875430.730.0270.0690.0632.2100
4.43-46.986.50.0631147617730.9890.0310.0820.07620.597.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.59 Å36.29 Å
Translation5.59 Å36.29 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALA3.3.22data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
iMOSFLM7.2.1data reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→36.29 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4917 4.93 %Random
Rwork0.1509 94731 --
obs0.1527 99648 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.81 Å2 / Biso mean: 23.4191 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 1.4→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 26 223 2253
Biso mean--40.06 36.41 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052187
X-RAY DIFFRACTIONf_angle_d0.8392990
X-RAY DIFFRACTIONf_chiral_restr0.074335
X-RAY DIFFRACTIONf_plane_restr0.006395
X-RAY DIFFRACTIONf_dihedral_angle_d8.5171198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.28851710.284931303301100
1.4159-1.43260.2811770.257131743351100
1.4326-1.45010.25081780.230731393317100
1.4501-1.46840.24021610.212231773338100
1.4684-1.48770.25421730.207431293302100
1.4877-1.50810.2381300.195331873317100
1.5081-1.52970.20571170.190332183335100
1.5297-1.55250.23761410.180832243365100
1.5525-1.57670.20211620.170931283290100
1.5767-1.60260.17521580.159931593317100
1.6026-1.63020.21241750.155231203295100
1.6302-1.65990.16621820.144631573339100
1.6599-1.69180.19181490.142531963345100
1.6918-1.72630.19421270.143931853312100
1.7263-1.76390.19111670.149431723339100
1.7639-1.80490.18331750.146931073282100
1.8049-1.850.25741950.143331933388100
1.85-1.90010.1871910.142831083299100
1.9001-1.9560.18031800.135531543334100
1.956-2.01910.18221700.133131483318100
2.0191-2.09120.16741930.128631463339100
2.0912-2.1750.16111850.128631423327100
2.175-2.27390.17041400.132731963336100
2.2739-2.39380.16461410.144831683309100
2.3938-2.54370.1721730.144931253298100
2.5437-2.74010.18571850.150331723357100
2.7401-3.01570.22091750.159631293304100
3.0157-3.45180.19441610.152731743335100
3.4518-4.34780.16491590.131631753334100
4.3478-36.30270.17311260.16163099322597

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