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Yorodumi- PDB-2jbg: crystal structure of the mutant N560A of the nuclease domain of C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jbg | ||||||
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Title | crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7 | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / ZINC / TOXIN / PLASMID / NUCLEASE / HYDROLASE / ANTIBIOTIC / H-N-H MOTIF / BACTERIOCIN / ENDONUCLEASE / METAL-BINDING / ANTIMICROBIAL / DNA HYDROLYSIS / BACTERIOCIN IMMUNITY / HIS METAL FINGER 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 / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Huang, H. / Yuan, H.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Conserved Asparagine in the Hnh Motif Serves an Important Structural Role in Metal Finger Endonucleases. Authors: Huang, H. / 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 | 2jbg.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbg.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbg ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbg | HTTPS FTP |
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-Related structure data
Related structure data | 2jazC 2jb0C 1mz8S S: Starting model for refinement C: citing same article (ref.) |
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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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Plasmid: PQE70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: Q03708, Hydrolases; Acting on ester bonds #2: Protein | Mass: 15019.079 Da / Num. of mol.: 2 / Fragment: NUCLEASE DOMAIN, RESIDUES 446-576 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Plasmid: PQE70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: Q47112, Hydrolases; Acting on ester bonds #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-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: 56.1 % |
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Crystal grow | pH: 4.6 Details: 20 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE TRIHYDRATE AT PH 4.6 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 2, 2004 / Details: MIRRORS |
Radiation | Monochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.4 Å / Num. obs: 29109 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.38 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MZ8 Resolution: 2.2→37.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 286152.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.6275 Å2 / ksol: 0.372362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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