[English] 日本語
![](img/lk-miru.gif)
- PDB-6hbs: Structure of PLP internal aldimine form of Sphingopyxis sp. MTA14... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6hbs | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein | ||||||
![]() | Aminopentol aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / PLP / fumonisin | ||||||
Function / homology | ![]() Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Campopiano, D.J. / Serpico, A. / Marles-Wright, J. | ||||||
![]() | ![]() Title: Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein Authors: Campopiano, D.J. / Serpico, A. / Marles-Wright, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 185.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 145 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1012.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1014.2 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hbvC ![]() 3bs8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 48331.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D2D3B2, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.48 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.0 0.1 M Ammonium Sulfate 30 % (w/v) Polyacrylate, sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.83 Å / Num. obs: 95437 / % possible obs: 99.56 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.0375 / Rrim(I) all: 0.068 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 3 % / Rmerge(I) obs: 0.6757 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 9514 / CC1/2: 0.712 / Rpim(I) all: 0.4555 / Rrim(I) all: 0.8182 / % possible all: 99.09 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3BS8 Resolution: 1.65→46.83 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.329 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.866 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→46.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|