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Yorodumi- PDB-2gze: Crystal structure of the E9 DNase domain with a mutant immunity p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gze | ||||||
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Title | Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A) | ||||||
Components |
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Keywords | Antibiotic/Antibiotic Inhibitor / Protein-protein complex / 4-helix bundle / DNase domain / HNH-motif / Antibiotic-Antibiotic Inhibitor COMPLEX | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Santi, P.S. / Kolade, O.O. / Kuhlmann, U.C. / Kleanthous, C. / Hemmings, A.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex of the Colicin E9 DNase Domain with a Mutant Immunity Protein, IM9 (Y55A) Authors: Kuhlmann, U.C. / Santi, P.S. / Kolade, O.O. / Kleanthous, C. / Hemmings, A.M. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structural and Mechanistic Basis of Immunity Towards Endonuclease Colicins Authors: Kleanthous, C. / Kuhlmann, U.C. / Pommer, A.J. / Ferguson, N. / E Radford, S. / Moore, G.R. / James, R. / 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 | 2gze.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gze.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gze ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gze | HTTPS FTP |
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-Related structure data
Related structure data | 1emvS 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
#1: Protein | Mass: 9500.404 Da / Num. of mol.: 1 / Mutation: Y55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: IMM9_ECOLI / Plasmid: pET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13479 |
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#2: Protein | Mass: 15120.021 Da / Num. of mol.: 1 / Fragment: Colicin E9,C-terminal Domain,DNase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: col, cei / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P09883, deoxyribonuclease I |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-PO4 / |
#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: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SILICON(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→25 Å / Num. all: 19600 / Num. obs: 19600 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Χ2: 1.294 / Net I/σ(I): 39 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMV Resolution: 1.8→22.38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.131 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.147 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.294 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→22.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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