+Open data
-Basic information
Entry | Database: PDB / ID: 1kyx | ||||||
---|---|---|---|---|---|---|---|
Title | Lumazine Synthase from S.pombe bound to carboxyethyllumazine | ||||||
Components | 6,7-Dimethyl-8-ribityllumazine SynthaseLumazine synthase | ||||||
Keywords | TRANSFERASE / riboflavin biosynthesis / lumazine synthase / Schizosaccharomyces pombe / ligand binding | ||||||
Function / homology | Function and homology information 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 | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gerhardt, S. / Haase, I. / Steinbacher, S. / Kaiser, J.T. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase. Authors: Gerhardt, S. / Haase, I. / Steinbacher, S. / Kaiser, J.T. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kyx.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kyx.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/1kyx ftp://data.pdbj.org/pub/pdb/validation_reports/ky/1kyx | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kyvC 1kyyC 1kz1C 1kz4C 1kz6C 1kz9C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17206.791 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UUB1, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CRM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: citrate, ammonium dihydrogen phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15.467 Å / Num. all: 32133 / Num. obs: 32116 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.74 Å / % possible all: 100 |
Reflection | *PLUS % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.42 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15.467 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15.467 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15.46 Å / % reflection Rfree: 10 % / Rfactor all: 0.178 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.175 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|