[English] 日本語
![](img/lk-miru.gif)
- PDB-4ade: Structural and functional study of succinyl-ornithine transaminas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ade | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and functional study of succinyl-ornithine transaminase from E. coli | ||||||
![]() | SUCCINYLORNITHINE TRANSAMINASE | ||||||
![]() | TRANSFERASE / PLP ENZYMES / AMINOTRANSFERASE | ||||||
Function / homology | ![]() succinylornithine transaminase / succinylornithine transaminase activity / ornithine catabolic process / arginine catabolic process to succinate / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine catabolic process to glutamate / arginine biosynthetic process via ornithine / arginine catabolic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J. / Peat, T.S. | ||||||
![]() | ![]() Title: Determination of the Structure of the Catabolic N-Succinylornithine Transaminase (Astc) from Escherichia Coli. Authors: Newman, J. / Seabrook, S. / Surjadi, R. / Williams, C.C. / Lucent, D. / Wilding, M. / Scott, C. / Peat, T.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 120.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4adbC ![]() 4adcC ![]() 4addC ![]() 2pb2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 43712.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P77581, succinyldiaminopimelate transaminase, succinylornithine transaminase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / pH: 5 Details: 1.4 M SODIUM MALONATE PH 7, 10% (V/V) MMT (MALATE-MES-TRIS) BUFFER AT PH 5.0, AT 293K WITH A PROTEIN TO CRYSTALLANT RATIO OF 3:1 IN THE PRESENCE OF SILVER BULLET SCREEN NUMBER 62. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→19.9 Å / Num. obs: 29220 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 22.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 6 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PB2 Resolution: 2.75→115.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.937 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.326 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→115.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|