[English] 日本語
![](img/lk-miru.gif)
- PDB-4adc: Structural and functional study of succinyl-ornithine transaminas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4adc | ||||||
---|---|---|---|---|---|---|---|
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 | ![]() | 319.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 260.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4adbC ![]() 4addC ![]() 4adeC ![]() 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.: 4 / Source method: isolated from a natural source / Details: NATIVE FROM E. COLI / Source: (natural) ![]() ![]() References: UniProt: P77581, succinylornithine transaminase, succinyldiaminopimelate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Nonpolymer details | PYRIDOXYL PHOSPHATE (PLP): PLP IS FREE FROM LYSINE 252 SCHIFF BASE | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 1.17 M SODIUM MALONATE PH 7.0, 0.09 M TRIS CHLORIDE PH 8.0, 0.02 M DI-ETHYLAMMONIUM FORMATE WITH DRY ORNITHINE POWDER ADDED DIRECTLY TO THE CRYSTAL DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.8 Å / Num. obs: 101215 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / % possible all: 86.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PB2 Resolution: 2.3→108.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.582 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.184 / 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: 23.519 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→108.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|