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Yorodumi- PDB-2gzi: Crystal Structure of the E9 DNase Domain with a Mutant Immunity P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gzi | ||||||
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Title | Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A) | ||||||
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: 1.7 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 (V34A) 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 | 2gzi.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gzi.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gzi ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gzi | 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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Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A SINGLE COPY OF THE BIOLOGICAL UNIT |
-Components
#1: Protein | Mass: 9564.447 Da / Num. of mol.: 1 / Mutation: V34A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: imm, ceiE9 / 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: 41.17 % |
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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, 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: 1.7→20 Å / Num. all: 23064 / Num. obs: 23064 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 / Χ2: 2.339 / Net I/σ(I): 23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1EMV Resolution: 1.7→19.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.972 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: Engh & Huber / 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: 24.983 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.739 Å / Total num. of bins used: 20
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