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- PDB-5ul8: Apo KPC-2 beta-lactamase crystal structure at 1.15 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5ul8
TitleApo KPC-2 beta-lactamase crystal structure at 1.15 Angstrom resolution
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / beta-lactamase / carbapenemase / Klebsiella / high-resolution
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
Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 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)R01AI103158-04 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 24, 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

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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)31,2836
Polymers30,8071
Non-polymers4765
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-40 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 60.200, 78.620
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-493-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.61 %
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: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→45.5 Å / Num. all: 93824 / Num. obs: 93824 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Rsym value: 0.078 / Net I/σ(I): 11 / Num. measured all: 605873
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
1.15-1.213.30.52542259128880.830.020.0510.047294.4
3.64-45.56.40.0472037332070.9980.0240.0650.062698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.6 Å32.14 Å
Translation5.6 Å32.14 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: 1.15→32.136 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 12.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1393 8886 5.05 %Random selection
Rwork0.1219 167207 --
obs0.1228 176093 96.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 17.0125 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: final / Resolution: 1.15→32.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 34 350 2410
Biso mean--28.18 31.96 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092214
X-RAY DIFFRACTIONf_angle_d1.0753037
X-RAY DIFFRACTIONf_chiral_restr0.084336
X-RAY DIFFRACTIONf_plane_restr0.009402
X-RAY DIFFRACTIONf_dihedral_angle_d12.906797
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 (%)
1.15-1.16310.29722710.2784072434371
1.1631-1.17680.28372410.2674398463977
1.1768-1.19110.23182710.24184766503783
1.1911-1.20620.24562800.23475092537288
1.2062-1.22210.22412440.21825298554292
1.2221-1.23880.20062660.19775583584996
1.2388-1.25650.20273160.17825644596099
1.2565-1.27530.18132980.156958156113100
1.2753-1.29520.17013060.149257646070100
1.2952-1.31640.15963010.140656845985100
1.3164-1.33910.15233020.135758416143100
1.3391-1.36350.15383490.131456686017100
1.3635-1.38970.16083230.134557596082100
1.3897-1.41810.1622920.130457626054100
1.4181-1.44890.15712760.126257536029100
1.4489-1.48260.14092780.110558086086100
1.4826-1.51970.12283100.09257676077100
1.5197-1.56080.11752830.092957396022100
1.5608-1.60670.11593350.089357696104100
1.6067-1.65850.10292960.085157476043100
1.6585-1.71780.10763070.089857646071100
1.7178-1.78660.12543140.092157506064100
1.7866-1.86790.11623150.093957676082100
1.8679-1.96640.1123230.093657046027100
1.9664-2.08950.10733220.093757166038100
2.0895-2.25080.11363520.097657386090100
2.2508-2.47730.1323020.104857696071100
2.4773-2.83560.12752560.112357936049100
2.8356-3.57180.13072980.126857776075100
3.5718-32.14880.15872590.14515700595998

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