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Yorodumi- PDB-5x5g: Crystal structure of TLA-3 extended-spectrum beta-lactamase in a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x5g | ||||||
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Title | Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / extended-spectrum beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wachino, J. / Jin, W. / Arakawa, Y. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2017 Title: Structural Insights into the TLA-3 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam and OP0595. Authors: Jin, W. / Wachino, J. / Yamaguchi, Y. / Kimura, K. / Kumar, A. / Yamada, M. / Morinaka, A. / Sakamaki, Y. / Yonezawa, M. / Kurosaki, H. / Arakawa, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x5g.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x5g.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/5x5g ftp://data.pdbj.org/pub/pdb/validation_reports/x5/5x5g | HTTPS FTP |
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-Related structure data
Related structure data | 5gs8SC 5gwaC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31346.771 Da / Num. of mol.: 1 / Fragment: UNP residues 30-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B6VPP7, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-OP0 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate, 2.8M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.22 Å / Num. obs: 18894 / % possible obs: 97 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2688 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GS8 Resolution: 2→55.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.525 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.633 Å2
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Refinement step | Cycle: 1 / Resolution: 2→55.22 Å
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Refine LS restraints |
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