[English] 日本語
![](img/lk-miru.gif)
- PDB-5b7s: Apo structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5b7s | ||||||
---|---|---|---|---|---|---|---|
Title | Apo structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 | ||||||
![]() | Cysteine desulfurase | ||||||
![]() | TRANSFERASE / Cysteine desulfurase / L-cysteine / Metabolic pathways | ||||||
Function / homology | ![]() cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ho, T.-H. / Kang, L.W. | ||||||
![]() | ![]() Title: Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the ArchaeonThermococcus onnurineus NA1. Authors: Ho, T.-H. / Huynh, K.-H. / Nguyen, D.Q. / Park, H. / Jung, K. / Sur, B. / Ahn, Y.-J. / Cha, S.-S. / Kang, L.-W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 170 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 482.3 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b7uC ![]() 5b87C ![]() 5b89C ![]() 1t3iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 46900.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: NA1 / Gene: TON_0289 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.33 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.03M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 0.1M Tris (base)/ Bicine pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→50 Å / Num. obs: 28968 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 7.1 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1T3I Resolution: 2.58→36.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.368 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.867 / ESU R Free: 0.371 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.06 Å2 / Biso mean: 52.856 Å2 / Biso min: 24.65 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.58→36.36 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.581→2.648 Å / Total num. of bins used: 20
|