[English] 日本語
![](img/lk-miru.gif)
- PDB-1l5l: Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)pu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1l5l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)purine and nicotinate | ||||||
![]() | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cheong, C.-G. / Escalante-Semerena, J. / Rayment, I. | ||||||
![]() | ![]() Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1l4nC ![]() 1l5fC ![]() 1l5kC ![]() 1l5mC ![]() 1l5nC ![]() 1lc5C ![]() 1lc7C ![]() 1lc8C ![]() 1d0sS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
Unit cell |
| ||||||||||
Details | The biological assembly is a dimer generated from one monomer in asymmetric unit by crystallographic two-fold axis |
-
Components
#1: Protein | Mass: 36675.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q05603, ![]() |
---|---|
#2: Chemical | ChemComp-7RP / |
#3: Chemical | ChemComp-NIO / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.21 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K |
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Details: double focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Highest resolution: 2 Å / Num. all: 20166 / Num. obs: 20166 / % possible obs: 89 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 3.3 / % possible all: 68 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1D0S Resolution: 2→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→500 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|