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- PDB-1nqu: Crystal Structure of Lumazine Synthase from Aquifex aeolicus in C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nqu | ||||||
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Title | Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase | ||||||
![]() | TRANSFERASE / Lumazine synthase / Aquifex aeolicus / inhibitor complex / vitamin biosynthesis / catalytic mechanism | ||||||
Function / homology | ![]() 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Meining, W. / Cushman, M. / Haase, I. / Fischer, M. / Bacher, A. / Ladenstein, R. | ||||||
![]() | ![]() Title: A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus. Authors: Zhang, X. / Meining, W. / Cushman, M. / Haase, I. / Fischer, M. / Bacher, A. / Ladenstein, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.8 KB | Display | ![]() |
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PDB format | ![]() | 140.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is an icosahedral capsid generated from the pentamer in the asymmetric unit by the I23 crystllographic symmetry operactions |
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Components
#1: Protein | Mass: 16727.201 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-RDL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium-potassium tartrate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8482 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.26 Å / Num. all: 97999 / Num. obs: 97592 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.75→1.78 Å / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 48.22 Å / Num. obs: 97916 / % possible obs: 99.9 % / Num. measured all: 735750 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.75→48.26 Å
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 48.22 Å | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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