[English] 日本語
![](img/lk-miru.gif)
- PDB-4ok9: Crystal structure of the single-stranded RNA binding protein HutP... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ok9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans | ||||||
![]() | Hut operon positive regulatory protein | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() L-histidine metabolic process / ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thiruselvam, V. / Ponnuswamy, M.N. / Kumarevel, T.S. | ||||||
![]() | ![]() Title: Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans Authors: Thiruselvam, V. / Sivaraman, P. / Kumarevel, T. / Ponnuswamy, M.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4okqC ![]() 2zh0 C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 16302.699 Da / Num. of mol.: 2 / Fragment: HutP Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NG80-2 / Gene: GTNG_0361, hutP / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.06 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 10%(W/V) PEG300, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 23, 2013 / Details: Si II crystal |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.91→50 Å / Num. all: 27972 / Num. obs: 27972 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 56 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1388 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 2ZH0 ![]() 2zh0 Resolution: 1.91→35.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.315 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.131 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 35.348 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→35.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.909→1.959 Å / Total num. of bins used: 20
|