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Yorodumi- PDB-1fr2: CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fr2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN IM9(E41A) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / protein-protein complex / Zinc containing enzyme / HNH-motif | ||||||
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 / Resolution: 1.6 Å | ||||||
Authors | Kuhlmann, U.C. / Pommer, A.J. / Moore, G.M. / James, R. / Kleanthous, C. / Hemmings, A.M. | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN IM9(E41A) Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.M. / James, R. / Kleanthous, C. / Hemmings, A.M. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.R. / James, R. / Kleanthous, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fr2.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fr2.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1fr2 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1fr2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a heterodimeric complex of the E9 DNase domain with the immunity protein Im9 |
-Components
#1: Protein | Mass: 9534.464 Da / Num. of mol.: 1 / Mutation: E41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21D (PRJ353) / Production host: Escherichia coli (E. coli) / References: UniProt: P13479 |
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#2: Protein | Mass: 15120.021 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, DNASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTRC99A (PKL14) / Production host: Escherichia coli (E. coli) / References: UniProt: P09883, deoxyribonuclease I |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-ZN / |
#5: 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: 2.05 Å3/Da / Density % sol: 40.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 24% PEG 4000, 0.1M sodium acetate, , pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 27531 / Num. obs: 26832 / % possible obs: 97.4 % / Redundancy: 4.96 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.195 / Num. unique all: 2467 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Resolution: 1.6→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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