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- PDB-1xn1: Crystal Structure Of Lumazine Synthase From Brucella Abortus (Ort... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xn1 | ||||||
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Title | Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms) | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase | ||||||
![]() | TRANSFERASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Klinke, S. / Zylberman, V. / Vega, D.R. / Guimaraes, B.G. / Braden, B.C. / Goldbaum, F.A. | ||||||
![]() | ![]() Title: Crystallographic studies on Decameric Brucella spp. Lumazine Synthase: A Novel Quaternary Arrangement Evolved for a New Function? Authors: Klinke, S. / Zylberman, V. / Vega, D.R. / Guimaraes, B.G. / Braden, B.C. / 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 | ![]() | 287.8 KB | Display | ![]() |
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PDB format | ![]() | 234.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 537.8 KB | Display | ![]() |
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Full document | ![]() | 591.7 KB | Display | |
Data in XML | ![]() | 57.4 KB | Display | |
Data in CIF | ![]() | 76.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1t13C ![]() 1di0S 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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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY ARE DIMERS OF PENTAMERS WHICH CAN BE OBTAINED APPLYING THE FOLLOWING OPERATIONS: TO CHAINS A,B,C,D,E: (1/2+X,3/2-Y,1-Z) ; TO CHAINS F,G,H,I,J: (-1/2+X,3/2-Y,1-Z) |
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Components
#1: Protein | Mass: 17381.900 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P61711, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 1.3M AMMONIUM SULFATE, 0.1M NA MES, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 20, 2004 / Details: SI SINGLE CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→56 Å / Num. all: 43004 / Num. obs: 43004 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 49.56 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.05→3.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6168 / Rsym value: 0.331 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DI0 Resolution: 3.05→56 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.53 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→56 Å
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Refine LS restraints |
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