+
Open data
-
Basic information
Entry | Database: PDB / ID: 4haa | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant | ||||||
![]() | Ribonuclease | ||||||
![]() | HYDROLASE / endoribonuclease | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Polyakov, K.M. / Trofimov, A.A. / Mitchevich, V.A. / Dorovatovskii, P.V. / Schulga, A.A. / Makarov, A.A. / Tkach, E.N. / Goncharuk, D.A. | ||||||
![]() | ![]() Title: Structure and functional studies of the ribonuclease binase Glu43Ala/Phe81Ala mutant. Authors: Mitkevich, V.A. / Schulga, A.A. / Trofimov, A.A. / Dorovatovskii, P.V. / Goncharuk, D.A. / Tkach, E.N. / Makarov, A.A. / Polyakov, K.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1govS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12093.490 Da / Num. of mol.: 4 / Fragment: UNP residues 54-162 / Mutation: E43A/F81A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00649, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 10, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.89→60 Å / Num. all: 37967 / Num. obs: 37967 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 | |||||||||||||||
Reflection shell | Resolution: 1.89→2.01 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.49 / Num. unique all: 5895 / % possible all: 89.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GOV Resolution: 1.9→18.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.02 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.062 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.027 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→18.73 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|