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Yorodumi- PDB-2jaz: CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jaz | ||||||
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Title | CRYSTAL STRUCTURE OF THE MUTANT N560D 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 | 2jaz.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jaz.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jaz_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 2jaz_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 2jaz_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 2jaz_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jaz ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jaz | HTTPS FTP |
-Related structure data
Related structure data | 2jb0C 2jbgC 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
#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: 15063.089 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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | pH: 7 Details: 20 % W/V PEG3350 AND 0.1 M DI-AMMONIUM HYDROGEN CITRATE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→37.48 Å / Num. obs: 35931 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.35 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MZ8 Resolution: 2.03→37.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 99948.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.4436 Å2 / ksol: 0.370187 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→37.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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