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Yorodumi- PDB-6fm6: Crystal structure of the class C beta-lactamase TRU-1 from Aeromo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fm6 | ||||||
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Title | Crystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / class C / serine beta-lactamase / TRU-1 / Aeromonas enteropelogenes | ||||||
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 | Aeromonas enteropelogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Pozzi, C. / De Luca, F. / Di Pisa, F. / Benvenuti, M. / Docquier, J.D. / Mangani, S. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Atomic-Resolution Structure of a Class C beta-Lactamase and Its Complex with Avibactam. Authors: Pozzi, C. / Di Pisa, F. / De Luca, F. / Benvenuti, M. / Docquier, J.D. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fm6.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fm6.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fm6 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fm6 | HTTPS FTP |
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-Related structure data
Related structure data | 6fm7C 4gzbS 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
#1: Protein | Mass: 41821.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas enteropelogenes (bacteria) / Gene: ampC / Plasmid: pET-TRU-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B2BSN6, UniProt: A0A175VLQ4*PLUS, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: 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: 1.98 Å3/Da / Density % sol: 38.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% wt/vol PEG-8000, 0.2 M ammonium sulfate and 0.1 M sodium cacodylate, pH 6.5 PH range: 6.5-7.5 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2007 |
Radiation | Monochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→38.35 Å / Num. obs: 141631 / % possible obs: 93.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 5.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.043 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 15018 / CC1/2: 0.967 / Rrim(I) all: 0.155 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GZB Resolution: 1.05→26.43 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / Rfactor Rfree error: 0.024 / SU B: 0.56 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0236 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / SU Rfree Cruickshank DPI: 0.0235 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.587 Å2
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Refine analyze | Luzzati coordinate error obs: 0.105 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.05→26.43 Å
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Refine LS restraints |
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