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Yorodumi- PDB-7cei: THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cei | ||||||
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Title | THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBITOR IM7 PROTEIN | ||||||
Components | (PROTEIN (COLICIN E7 IMMUNITY PROTEIN)) x 2 | ||||||
Keywords | IMMUNE SYSTEM / DNASE / E-GROUP COLICINS / PROTEIN-PROTEIN INTERACTION / PROTEIN RECOGNITION | ||||||
Function / homology | Function and homology information extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K12 substr. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ko, T.P. / Liao, C.C. / Ku, W.Y. / Chak, K.F. / Yuan, H.S. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Authors: Ko, T.P. / Liao, C.C. / Ku, W.Y. / Chak, K.F. / Yuan, H.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: The Crystal Structure of the Immunity Protein of Colicin E7 Suggests a Possible Colicin-Interacting Surface. Authors: Chak, K.-F. / Safo, M.K. / Ku, W.-Y. / Hsieh, S.-Y. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cei.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cei.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 7cei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7cei ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7cei | HTTPS FTP |
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-Related structure data
Related structure data | 1ceiS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9906.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria) Species: Escherichia coli / Strain: W3110 / Gene: CEIE7 / Gene (production host): CEIE7 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q03708 |
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#2: Protein | Mass: 23465.652 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE DOMAIN / Source method: isolated from a natural source Source: (natural) Escherichia coli str. K12 substr. (bacteria) Plasmid: PCOLE7 / Species: Escherichia coli / Strain: W3110 / References: UniProt: Q47112 |
#3: Chemical | ChemComp-ZN / |
#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: 2.8 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 15 MG/ML PROTEIN COMPLEX, 5 MM NA CITRATE, 0.25 M NH4 ACETATE, 10% PEG4000, PH 6.0 VAPOR DIFFUSION AGAINST 22.5% PEG4000 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 54 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 12090 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2 / Rsym value: 0.191 / % possible all: 76.3 |
Reflection | *PLUS Num. measured all: 38306 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CEI Resolution: 2.3→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 37.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.314 / % reflection Rfree: 8 % / Rfactor Rwork: 0.305 |