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Yorodumi- PDB-5tfq: Crystal structure of a representative of class A beta-lactamase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tfq | ||||||
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Title | Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Bacteroides cellulosilyticus DSM 14838 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.07 Å | ||||||
Authors | Nocek, B. / Hatzos-Skintges, C. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838 Authors: Nocek, B. / Hatzos-Skintges, C. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tfq.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tfq.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 5tfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tfq_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 5tfq_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 5tfq_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5tfq_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/5tfq ftp://data.pdbj.org/pub/pdb/validation_reports/tf/5tfq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31076.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria) Gene: BACCELL_03967 / Production host: Escherichia coli (E. coli) / References: UniProt: E2NI36, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.4 M NaH2PO4/1.6 M K2HPO4 0.1 M Imidazole:HCl pH 8.0 0.2 M Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2016 |
Radiation | Monochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→40 Å / Num. obs: 133512 / % possible obs: 98.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Net I/av σ(I): 30.75 / Net I/σ(I): 35 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.07→40 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.639 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / 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: 19.478 Å2
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Refinement step | Cycle: 1 / Resolution: 1.07→40 Å
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Refine LS restraints |
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