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Yorodumi- PDB-1cz0: INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cz0 | ||||||
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Title | INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / DISTORTED DNA / HIS-CYS BOX ZINC BINDING SITE / BETA SHEET DNA BINDING / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | Physarum polycephalum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Galburt, E.A. / Chevalier, B. / Jurica, M.S. / Flick, K.E. / Stoddard, B.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: A novel endonuclease mechanism directly visualized for I-PpoI. Authors: Galburt, E.A. / Chevalier, B. / Tang, W. / Jurica, M.S. / Flick, K.E. / Monnat Jr., R.J. / 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 | 1cz0.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cz0.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cz0_validation.pdf.gz | 379.8 KB | Display | wwPDB validaton report |
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Full document | 1cz0_full_validation.pdf.gz | 382.6 KB | Display | |
Data in XML | 1cz0_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1cz0_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1cz0 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1cz0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6437.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: I-PPOI DNA HOMING SEQUENCE #2: Protein | Mass: 17680.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q94702, Hydrolases; Acting on ester bonds #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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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: 3.42 Å3/Da / Density % sol: 64.04 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 3350, SODIUM CITRATE, SODIUM CHLORIDE, SPERMINE, EDTA, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 unknown / Method: vapor diffusion, hanging drop / Details: Flick, K.E., (1997) Protein Sci., 6, 2677. / PH range low: 5.8 / PH range high: 5.4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 |
Detector | Type: OTHER / Detector: CCD / Date: Apr 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 38078 / Num. obs: 38078 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.178 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. measured all: 206866 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 6 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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