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Open data
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Basic information
Entry | Database: PDB / ID: 1kyv | ||||||
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Title | Lumazine Synthase from S.pombe bound to riboflavin | ||||||
![]() | 6,7-Dimethyl-8-ribityllumazine Synthase | ||||||
![]() | TRANSFERASE / riboflavin biosynthesis / lumazine synthase / Schizosaccharomyces pombe / ligand binding | ||||||
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 | ![]() ![]() | ||||||
![]() | Gerhardt, S. / Haase, I. / Steinbacher, S. / Kaiser, J.T. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.2 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kyxC ![]() 1kyyC ![]() 1kz1C ![]() 1kz4C ![]() 1kz6C ![]() 1kz9C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17206.791 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pNCO113 / Production host: ![]() ![]() References: UniProt: Q9UUB1, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-RBF / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: citrate, sodium formate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
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: 2.4→16.03 Å / Num. all: 41051 / Num. obs: 40966 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.53 Å / % possible all: 99.8 |
Reflection | *PLUS % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.45 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.4→16.03 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.189 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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