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- PDB-8aki: Acyl-enzyme complex of ampicillin bound to deacylation mutant KPC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aki | |||||||||
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Title | Acyl-enzyme complex of ampicillin bound to deacylation mutant KPC-2 (E166Q) | |||||||||
![]() | Carbapenem-hydrolyzing beta-lactamase KPC | |||||||||
![]() | ANTIMICROBIAL PROTEIN / acyl-enzyme complex / antibiotic resistance / beta-lactamase / antibiotic / ligand | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tooke, C.L. / Hinchliffe, P. / Spencer, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Tautomer-Specific Deacylation and Omega-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 beta-Lactamase. Authors: Tooke, C.L. / Hinchliffe, P. / Beer, M. / Zinovjev, K. / Colenso, C.K. / Schofield, C.J. / Mulholland, A.J. / Spencer, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.3 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.8 KB | Display | ![]() |
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Full document | ![]() | 789.2 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8akjC ![]() 8akkC ![]() 8aklC ![]() 8akmC ![]() 6z21S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30805.646 Da / Num. of mol.: 1 / Mutation: E166Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-AIX / ( | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium Sulphate, 5% v/v ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89996 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.12 Å / Num. obs: 54082 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 13.46 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2714 / CC1/2: 0.613 / Rpim(I) all: 0.665 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Z21 Resolution: 1.4→48.12 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.49 Å2 / Biso mean: 21.9713 Å2 / Biso min: 10.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→48.12 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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