[English] 日本語
![](img/lk-miru.gif)
- PDB-5g2p: The crystal structure of a S-selective transaminase from Arthroba... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5g2p | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a S-selective transaminase from Arthrobacter sp. | ||||||
![]() | TRANSAMINASE | ||||||
![]() | TRANSFERASE / TRANSAMINASE | ||||||
Function / homology | ![]() Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases Authors: Van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha Van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 382.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 312.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 488.1 KB | Display | |
Data in XML | ![]() | 74.4 KB | Display | |
Data in CIF | ![]() | 108.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g09C ![]() 5g0aC ![]() 5g2qC ![]() 3gjuS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54203.145 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND LYS298 / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A1C7D191*PLUS, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % / Description: NONE |
---|---|
Crystal grow | pH: 5 Details: 15% PEG3350 0.2 M NA-MALONATE 100 MM MMT BUFFER (DL-MALIC ACID, MES AND TRIS BASE) PH 5.0) 10 MM PLP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.1 Å / Num. obs: 137172 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.2 / % possible all: 92.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GJU Resolution: 1.89→46.84 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.611 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.645 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→46.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|