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Yorodumi- PDB-1nqw: Crystal Structure of Lumazine Synthase from Aquifex aeolicus in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nqw | ||||||
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Title | Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid | ||||||
Components | 6,7-dimethyl-8-ribityllumazine synthase | ||||||
Keywords | TRANSFERASE / Lumazine synthase / Aquifex aeolicus / inhibitor complex / vitamin biosynthesis / catalytic mechanism | ||||||
Function / homology | Function and homology information 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 | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhang, X. / Meining, W. / Cushman, M. / Haase, I. / Fischer, M. / Bacher, A. / Ladenstein, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqw.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqw.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqw ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 |
-Components
#1: Protein | Mass: 16727.201 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-5YL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 400, lithium sulphate, MOPS, pH 6.5, 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8482 Å |
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: 2.2→48.13 Å / Num. all: 49207 / Num. obs: 49207 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.2→2.24 Å / % possible all: 100 |
Reflection | *PLUS Num. obs: 49238 / Num. measured all: 377239 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.13 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→48.13 Å
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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