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Yorodumi- PDB-6fm7: Crystal structure of the class C beta-lactamase TRU-1 from Aeromo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fm7 | ||||||
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Title | Crystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes in complex with avibactam | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / avibactam / NXL / serine beta-lactamase / TRU-1 / class C / 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: 1.04 Å | ||||||
Authors | Pozzi, C. / De Luca, F. / Benvenuti, M. / Di Pisa, F. / 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 | 6fm7.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fm7.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6fm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fm7_validation.pdf.gz | 812.6 KB | Display | wwPDB validaton report |
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Full document | 6fm7_full_validation.pdf.gz | 813.5 KB | Display | |
Data in XML | 6fm7_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6fm7_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fm7 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fm7 | HTTPS FTP |
-Related structure data
Related structure data | 6fm6SC 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 | ChemComp-NXL / ( | ||||
#3: Chemical | #4: Chemical | #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: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% 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: ID23-1 / Wavelength: 0.9834 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9834 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→46.33 Å / Num. obs: 153026 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 6.525 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.04→1.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 20705 / CC1/2: 0.934 / Rrim(I) all: 0.379 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FM6 Resolution: 1.04→46.31 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Rfactor Rfree error: 0.022 / SU B: 0.498 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0213 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / SU Rfree Cruickshank DPI: 0.0224 / 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: 10.812 Å2
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Refine analyze | Luzzati coordinate error obs: 0.109 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.04→46.31 Å
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Refine LS restraints |
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