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- PDB-6bvs: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bvs | ||||||||||||
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Title | Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A from Cupriavidus metallidurans in complex with 4-Cl-3-HAA | ||||||||||||
![]() | 3-hydroxyanthranilate 3,4-dioxygenase | ||||||||||||
![]() | OXIDOREDUCTASE / Complex structure / Dioxygenase / Mutant I142A | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Yang, Y. / Liu, F. / Liu, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. Authors: Yang, Y. / Liu, F. / 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 | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bvpC ![]() 6bvqC ![]() 6bvrC ![]() 6cd3C ![]() 6d60C ![]() 6d61C ![]() 6d62C ![]() 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: 22548.297 Da / Num. of mol.: 1 / Mutation: I142A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||
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#2: Chemical | ChemComp-4AA / | ||
#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000 13%, 0.1M Tris-HCl, 0.2 M MgCl2, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 12, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.31→50 Å / Num. obs: 10918 / % possible obs: 99.9 % / Redundancy: 17.6 % / Biso Wilson estimate: 40.88 Å2 / Rmerge(I) obs: 0.211 / Χ2: 1.09 / Net I/σ(I): 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YFU Resolution: 2.318→42.197 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.34 Å2 / Biso mean: 46.1269 Å2 / Biso min: 26.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.318→42.197 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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