+
Open data
-
Basic information
Entry | Database: PDB / ID: 7w05 | ||||||
---|---|---|---|---|---|---|---|
Title | 12 mutant Ribonuclease from Hericium erinaceus GMP binding form | ||||||
![]() | Ribonuclease T1 | ||||||
![]() | DNA BINDING PROTEIN / catalytic activity enzyme anti tumor activity nucleic acid binding RNA binding | ||||||
Function / homology | : / : / Ribonuclease/ribotoxin / RNA nuclease activity / RNA binding / metal ion binding / GUANOSINE / DI(HYDROXYETHYL)ETHER / Ribonuclease T1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takebe, K. / Chida, T. / Suzuki, M. / Itagaki, T. / Morita, Y. / Uzawa, N. / Kobayashi, H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: 12 mutant Ribonuclease from Hericium erinaceus GMP binding form Authors: Takebe, K. / Chida, T. / Suzuki, M. / Uzawa, N. / Kobayashi, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6ls1S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10703.474 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GMP / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→46.31 Å / Num. obs: 22027 / % possible obs: 98.77 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 33.78 |
Reflection shell | Resolution: 1.19→1.21 Å / Num. unique obs: 1444 / CC1/2: 0.821 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6LS1 Resolution: 1.29→11.9947 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.02 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.79 Å2 / Biso mean: 15.4588 Å2 / Biso min: 6.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.29→11.9947 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
|