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- PDB-2o6h: Lumazine synthase RibH1 from Brucella melitensis (Gene BMEI1187, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o6h | ||||||
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Title | Lumazine synthase RibH1 from Brucella melitensis (Gene BMEI1187, Swiss-Prot entry Q8YGH2) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase 1 | ||||||
![]() | TRANSFERASE / lumazine synthase | ||||||
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 | ![]() | 149 KB | Display | ![]() |
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PDB format | ![]() | 118.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f59SC ![]() 2i0fC ![]() 2obxC 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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Unit cell |
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Components
#1: Protein | Mass: 16826.791 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8YGH2, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-CA / #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: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 22% PEG 400, 0.2M CaCl2, 0.1M MES, pH 6.3, 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: 2.7→48.8 Å / Num. all: 27278 / Num. obs: 22799 / % possible obs: 83.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3174 / Rsym value: 0.313 / % possible all: 82.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F59 Resolution: 2.7→48.8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.68 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.8 Å
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Refine LS restraints |
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