[English] 日本語
![](img/lk-miru.gif)
- PDB-5b3a: Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5b3a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate | ||||||
![]() | Protein CysO | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Takeda, E. / Kawai, Y. / Kataoka, M. / Ishikawa, K. | ||||||
![]() | ![]() Title: Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1 Authors: Takeda, E. / Kunimoto, K. / Kawai, Y. / Kataoka, M. / Ishikawa, K. / Nakamura, T. #1: ![]() Title: Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1 Authors: Nakamura, T. / Kawai, Y. / Kunimoto, K. / Iwasaki, Y. / Nishii, K. / Kataoka, M. / Ishikawa, K. #2: ![]() Title: Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution Authors: Oda, Y. / Mino, K. / Ishikawa, K. / Ataka, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 167.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5b36C ![]() 3vsaS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42025.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9YBL2, ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
---|---|
Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 27% 2-propanol, 12% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 5% MPD as a cryoprotectant, 20 mM O-phospho-L-serine (OPS) and 12 mM TCEP-HCl |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Nov 24, 2009 |
Radiation | Monochromator: Rotated-inclined double-crystal monochromator , Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.14→32.92 Å / Num. obs: 40639 / % possible obs: 97.99 % / Redundancy: 10 % / Net I/σ(I): 59.8 |
Reflection shell | Resolution: 2.14→2.18 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: CysO free form (PDB ID, 3VSA) Resolution: 2.14→32.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.821 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.593 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.14→32.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|