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- PDB-6vi9: Observing a ring-cleaving dioxygenase in action through a crystal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vi9 | |||||||||||||||
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Title | Observing a ring-cleaving dioxygenase in action through a crystalline lens - an alkylperoxo bound structure | |||||||||||||||
![]() | 3-hydroxyanthranilate 3,4-dioxygenase | |||||||||||||||
![]() | OXIDOREDUCTASE / In crystallo reaction / Extradiol dioxygenase / NAD+ biosynthesis / Intermediate | |||||||||||||||
Function / homology | ![]() 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / ferrous iron binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Wang, Y. / Liu, F. / Yang, Y. / Liu, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Authors: Wang, Y. / Liu, K.F. / Yang, Y. / Davis, I. / Liu, 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 | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 348.7 KB | Display | ![]() |
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Full document | ![]() | 348.7 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 4.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vi5C ![]() 6vi6C ![]() 6vi7C ![]() 6vi8C ![]() 6viaC ![]() 6vibC ![]() 6x11C ![]() 1yfuS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22590.377 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: nbaC, Rmet_5193 / Production host: ![]() ![]() References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-QXM / ( |
#4: Chemical | ChemComp-TRS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 15% PEG8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 11036 / % possible obs: 99.6 % / Redundancy: 16.7 % / Biso Wilson estimate: 26.38 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.996 / Num. unique obs: 478 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YFU Resolution: 2.31→30.55 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→30.55 Å
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Refine LS restraints |
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LS refinement shell |
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