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Yorodumi- PDB-3qqy: Crystal structure of a novel LAGLIDADG homing endonuclease, I-Onu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qqy | ||||||
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Title | Crystal structure of a novel LAGLIDADG homing endonuclease, I-OnuI (from Ophiostoma novo-ulmi subsp. americana) | ||||||
Components |
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Keywords | HYDROLASE/DNA / Protein-DNA comlex / LAGLIDADG family / Hydrolase / DNA binding / Mitochondrion / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ophiostoma novo-ulmi subsp. americana (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Takeuchi, R. / Stoddard, B.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Tapping natural reservoirs of homing endonucleases for targeted gene modification. Authors: Takeuchi, R. / Lambert, A.R. / Mak, A.N. / Jacoby, K. / Dickson, R.J. / Gloor, G.B. / Scharenberg, A.M. / Edgell, D.R. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qqy.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qqy.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qqy_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 3qqy_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 3qqy_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3qqy_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/3qqy ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qqy | HTTPS FTP |
-Related structure data
Related structure data | 3r7pC 1p8kS 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: 35174.859 Da / Num. of mol.: 1 / Fragment: UNP Residues 413-715 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ophiostoma novo-ulmi subsp. americana (fungus) Gene: rps3/HEG fusion / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q4VWW5 |
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#2: DNA chain | Mass: 7759.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Target sequence for the co-crystallized protein |
#3: DNA chain | Mass: 8213.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Target sequence for the co-crystallized protein |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 mM sodium acetate, 100 mM ammonium sulfate, 25% PEG 300, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 19182 / Num. obs: 18568 / % possible obs: 96.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.62 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P8K Resolution: 2.401→44.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.343 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.267 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.558 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→44.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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