[English] 日本語
Yorodumi- PDB-1bxi: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bxi | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / COLICINS / ENDONUCLEASE / PROTEIN-PROTEIN INTERACTION | ||||||
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 / protein domain specific binding / protein-containing complex / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Kuhlmann, U.C. / Kleanthous, C. / James, R. / Moore, G.R. / Hemmings, A.M. | ||||||
Citation | Journal: Thesis / Year: 1998 Title: Crystal Structure of the E.Coli Colicin E9 DNase Domain With its Cognate Immunity Protein Im9 Authors: Kuhlmann, U.C. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structural and Mechanistic Basis of Immunity Toward Endonuclease Colicins Authors: Kleanthous, C. / Kuhlmann, U.C. / Pommer, A.J. / Radford, N.Ferguson S.E. / Moore, G.R. / James, R. / Hemmings, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bxi.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bxi.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1bxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bxi_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bxi_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 1bxi_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1bxi_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bxi ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bxi | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9524.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: E9IMM / Plasmid: PRJ345 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P13479 |
---|---|
#2: Protein | Mass: 15213.811 Da / Num. of mol.: 1 / Fragment: DNASE DOMAIN, RESIDUES 450-581 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COLE9 / Plasmid: PRJ353 / Gene (production host): COLE9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 (DE3) / References: UniProt: P09883 |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.4 % |
---|---|
Crystal grow | pH: 5.3 / Details: 24%(W/V)PEG 4K, 0.1MM SODIUM-ACETATE, PH5.3 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.979,0.9795,0.9 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.05→20 Å / Num. obs: 13096 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 22.8 | ||||||||||||
Reflection shell | Resolution: 2.05→2.15 Å / Mean I/σ(I) obs: 6.7 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.05→8 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|