[English] 日本語
![](img/lk-miru.gif)
- PDB-1n07: Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1n07 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold | ||||||
![]() | PUTATIVE riboflavin kinase | ||||||
![]() | TRANSFERASE / kinase / phosphoryl transferases / flavin cofactors / metal binding | ||||||
Function / homology | ![]() Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / mitochondrial inner membrane / mitochondrion / zinc ion binding / ATP binding ...Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / mitochondrial inner membrane / mitochondrion / zinc ion binding / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bauer, S. / Kemter, K. / Bacher, A. / Huber, R. / Fischer, M. / Steinbacher, S. | ||||||
![]() | ![]() Title: Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold Authors: Bauer, S. / Kemter, K. / Bacher, A. / Huber, R. / Fischer, M. / Steinbacher, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1n05SC ![]() 1n06C ![]() 1n08C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18938.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPCC18.16C / Plasmid: pNCO / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 2002 / Details: mirror |
Radiation | Monochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. all: 11694 / Num. obs: 11694 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.041 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.242 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 93.9 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1N05 Resolution: 2.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.227 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|