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- PDB-2obx: Lumazine synthase RibH2 from Mesorhizobium loti (Gene mll7281, Sw... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2obx | ||||||
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Title | Lumazine synthase RibH2 from Mesorhizobium loti (Gene mll7281, Swiss-Prot entry Q986N2) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase 1 | ||||||
![]() | TRANSFERASE / lumazine synthase / alpha-beta | ||||||
Function / homology | ![]() 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klinke, S. / Zylberman, V. / Bonomi, H.R. / Haase, I. / Guimaraes, B.G. / Braden, B.C. / Bacher, A. / Fischer, M. / Goldbaum, F.A. | ||||||
![]() | ![]() Title: Structural and kinetic properties of lumazine synthase isoenzymes in the order rhizobiales Authors: Klinke, S. / Zylberman, V. / Bonomi, H.R. / Haase, I. / Guimaraes, B.G. / Braden, B.C. / Bacher, A. / Fischer, M. / Goldbaum, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290 KB | Display | ![]() |
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PDB format | ![]() | 237.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 81.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f59C ![]() 2i0fC ![]() 2o6hC ![]() 1t13S S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17304.570 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q986N2, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-INI / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 16% PEG 4000, 15% isopropanol, 20mM sodium/potassium phosphate pH 7.0, 0.1M ammonium sulfate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 26, 2006 |
Radiation | Monochromator: SI double crystal monocromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→87.7 Å / Num. all: 46427 / Num. obs: 46427 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.53→2.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6236 / Rsym value: 0.255 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1T13 Resolution: 2.53→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→50 Å
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Refine LS restraints |
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