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Yorodumi- PDB-1e44: ribonuclease domain of colicin E3 in complex with its immunity protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+44 | ||||||
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Title | ribonuclease domain of colicin E3 in complex with its immunity protein | ||||||
Components |
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Keywords | RIBONUCLEASE / INHIBITION / PROTEIN-PROTEIN INTERACTIONS / RIBOSOME INACTIVATION / TOXIN | ||||||
Function / homology | Function and homology information negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / defense response to bacterium / RNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Carr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Inhibition of a Ribosome Inactivating Ribonuclease: The Crystal Structure of the Cytotoxic Domain of Colicin E3 in Complex with its Immunity Protein Authors: Carr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e44.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e44.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1e44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e44 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e44 | HTTPS FTP |
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-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: 9910.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02984 |
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#2: Protein | Mass: 10812.117 Da / Num. of mol.: 1 / Fragment: RIBONUCLEASE DOMAIN RESIDUES 456-551 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) Description: CO-EXPRESSED WITH A HIS-TAGGED IMMUNITY PROTEIN Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00646 |
#3: Chemical | ChemComp-EDO / |
#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: 4.39 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 0.1 M NA CITRATE PH 5.6, 20% ISOPROPANOL, 10% PEG 4000 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Carr, S., (1999) Acta Crystallogr., D56, 1630. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9, 0.97, 0.979 | ||||||||||||
Detector | Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. obs: 14892 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.039 / Net I/σ(I): 37.8 | ||||||||||||
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.237 / % possible all: 97.5 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.039 | ||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.237 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→30 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.45 Å / Rfactor Rfree: 0.229 / Rfactor obs: 0.194 |