+
Open data
-
Basic information
Entry | Database: PDB / ID: 1l4b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of CobT in apo state | ||||||
![]() | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / CobT / cobalamin synthetic enzyme / phosphoribosyltransferase / 5 / 6-dimethylbenzimidazole / nicotinate mononucleotide | ||||||
Function / homology | ![]() nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cheong, C.-G. / Escalante-Semerena, J. / Rayment, I. | ||||||
![]() | ![]() Title: Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 74.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1l4eC ![]() 1l4fC ![]() 1l4gC ![]() 1l4hC ![]() 1l4kC ![]() 1l4lC ![]() 1l4mC ![]() 1l5oC ![]() 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, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.55 % |
---|---|
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: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å / Num. obs: 31865 / % possible obs: 88.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 1.6 / % possible all: 60.6 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1D0S Resolution: 1.7→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→500 Å
| ||||||||||||||||||||
Refine LS restraints |
|