[English] 日本語
![](img/lk-miru.gif)
- PDB-6x1j: The homing endonuclease I-WcaI bound to its DNA recognition sequence -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6x1j | ||||||
---|---|---|---|---|---|---|---|
Title | The homing endonuclease I-WcaI bound to its DNA recognition sequence | ||||||
![]() |
| ||||||
![]() | HYDROLASE / intron-encoded DNA homing endonuclease / enzyme / protein-DNA interactions / isoschizomers | ||||||
Function / homology | ![]() intron homing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nawimanage, R. / Lohman, J.R. / Gimble, F.S. | ||||||
![]() | ![]() Title: Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Targets with Dissimilar Rates and Specificities. Authors: Nawimanage, R.R. / Yuan, Z. / Casares, M. / Joshi, R. / Lohman, J.R. / Gimble, F.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r7mS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 27855.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q34807, Hydrolases; Acting on ester bonds | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 7741.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: DNA chain | Mass: 7615.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % / Description: Needles |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 21% PEG 3350, 0.1M Tris-HCl, 0.2M Lithium sulfate, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 17, 2016 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.945→30 Å / Num. obs: 33735 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.964 / CC star: 0.991 / Rpim(I) all: 0.104 / Rrim(I) all: 0.198 / Χ2: 1.063 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.945→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3306 / CC1/2: 0.807 / CC star: 0.945 / Rpim(I) all: 0.461 / Rrim(I) all: 0.858 / Χ2: 0.882 / % possible all: 99.6 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1R7M Resolution: 1.945→29.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.699 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.33 Å2 / Biso mean: 37.752 Å2 / Biso min: 12.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.945→29.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9451→1.996 Å / Rfactor Rfree error: 0
|