[English] 日本語
![](img/lk-miru.gif)
- PDB-1cyq: INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1cyq | ||||||
---|---|---|---|---|---|---|---|
Title | INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / DISTORTED DNA / HIS-CYS BOX ZINC BINDING SITE / BETA SHEET DNA BINDING / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Galburt, E.A. / Chevalier, B. / Jurica, M.S. / Flick, K.E. / Stoddard, B.L. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 379.9 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
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: 17612.979 Da / Num. of mol.: 2 / Mutation: H98A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q94702, Hydrolases; Acting on ester bonds #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3350, SODIUM CITRATE, SODIUM CHLORIDE, SPERMINE, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: Flick, K.E., (1997) Protein Sci., 6, 2677. / PH range low: 5.8 / PH range high: 5.4 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 49539 / Num. obs: 49539 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.302 / % possible all: 82.2 |
Reflection | *PLUS Num. measured all: 171353 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 82.2 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.93→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→50 Å
| |||||||||||||||||||||||||
Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 6 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|