[English] 日本語
![](img/lk-miru.gif)
- PDB-2a57: Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2a57 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase | ||||||
![]() | TRANSFERASE / 6 / 7-dimethyl-8-ribityllumazine synthase / riboflavin / riboflavin biosynthesis / LUSY | ||||||
Function / homology | ![]() riboflavin synthase activity / riboflavin binding / 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / mitochondrial intermembrane space / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koch, M. / Breithaupt, C. / Gerhardt, S. / Haase, I. / Weber, S. / Cushman, M. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
![]() | ![]() Title: Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase Authors: Koch, M. / Breithaupt, C. / Gerhardt, S. / Haase, I. / Weber, S. / Cushman, M. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 149.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2a58C ![]() 2a59C ![]() 1kyvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | the biological assembly is the pentamer found in the asymmetric unit |
-
Components
#1: Protein | Mass: 17183.756 Da / Num. of mol.: 5 / Mutation: W27Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rib4 / Production host: ![]() ![]() References: UniProt: Q9UUB1, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-CRM / #3: Chemical | ChemComp-PO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: sodium citrate, ammonium dihydrogen phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→20 Å / Num. all: 26937 / Num. obs: 26937 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.75→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.517 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KYV Resolution: 2.75→25 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 58.754 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.234 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|