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Yorodumi- PDB-1tfk: Ribonuclease from Escherichia coli complexed with its inhibtor protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tfk | ||||||
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Title | Ribonuclease from Escherichia coli complexed with its inhibtor protein | ||||||
Components |
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Keywords | TOXIN/TOXIN INHIBITOR / PROTEIN-PROTEIN COMPLEX / TOXIN-TOXIN INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / RNA nuclease activity / killing of cells of another organism / defense response to bacterium Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Yajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Kezuka, Y. / Hidaka, M. / Nonaka, T. / Ohsawa, K. / Masaki, H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Relation between tRNase activity and the structure of colicin D according to X-ray crystallography Authors: Yajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Hidaka, M. / Kezuka, Y. / Nonaka, T. / Ohsawa, K. / Masaki, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tfk.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tfk.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 1tfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tfk_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 1tfk_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 1tfk_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1tfk_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/1tfk ftp://data.pdbj.org/pub/pdb/validation_reports/tf/1tfk | HTTPS FTP |
-Related 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: 10831.103 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDA / Production host: Escherichia coli (E. coli) / References: UniProt: P17998 |
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#2: Protein | Mass: 10631.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Inhibitor protein / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDI / Production host: Escherichia coli (E. coli) / References: UniProt: P11899 |
#3: Chemical | ChemComp-MES / |
#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: 2.67 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, DTT, magnesium acetate, MES, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97919, 0.97937, 0.98200 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 27, 2003 | ||||||||||||
Radiation | Monochromator: the rotated-inclined double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→23.1 Å / Num. all: 15888 / Num. obs: 15793 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→23.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→23.1 Å
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Refine LS restraints |
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