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Yorodumi- PDB-2a8k: Structural and Mutational Studies of the Catalytic Domain of Coli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a8k | ||||||
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Title | Structural and Mutational Studies of the Catalytic Domain of Colicin E5a tRNA-Specific Ribonuclease | ||||||
Components | Colicin E5 | ||||||
Keywords | HYDROLASE / Ribonuclease / Toxin | ||||||
Function / homology | Function and homology information RNA nuclease activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Lin, Y.L. / Elias, Y. / Huang, R.H. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural and mutational studies of the catalytic domain of colicin E5: A tRNA-specific ribonuclease Authors: Lin, Y.L. / Elias, Y. / Huang, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a8k.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a8k.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 2a8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a8k_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 2a8k_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 2a8k_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2a8k_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a8k ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a8k | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11996.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col / Plasmid: PLM1-ColE5 / Production host: Escherichia coli (E. coli) References: UniProt: P18000, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-CA / #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: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9794, 0.9792, 0.9686 | ||||||||||||
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2003 | ||||||||||||
Radiation | Monochromator: Yale Mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→30 Å / Num. all: 76723 / Num. obs: 73778 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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