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Yorodumi- PDB-6dpt: X-ray crystal structure of AmpC beta-lactamase with nanomolar inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dpt | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase with nanomolar inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / AmpC beta-lacatamase / inhibitor complex / phenolate / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Singh, I. | ||||||
Citation | Journal: Nature / Year: 2019 Title: Ultra-large library docking for discovering new chemotypes. Authors: Lyu, J. / Wang, S. / Balius, T.E. / Singh, I. / Levit, A. / Moroz, Y.S. / O'Meara, M.J. / Che, T. / Algaa, E. / Tolmachova, K. / Tolmachev, A.A. / Shoichet, B.K. / Roth, B.L. / Irwin, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dpt.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dpt.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/6dpt ftp://data.pdbj.org/pub/pdb/validation_reports/dp/6dpt | HTTPS FTP |
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-Related structure data
Related structure data | 6dpxC 6dpyC 6dpzC 1ke4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 1.7 M potassium phosphate, pH 8.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→87.87 Å / Num. obs: 75002 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4399 / CC1/2: 0.613 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KE4 Resolution: 1.79→87.866 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.58 Å2 / Biso mean: 34.808 Å2 / Biso min: 18.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→87.866 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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