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Yorodumi- PDB-6vi7: Probing extradiol dioxygenase mechanism in NAD(+) biosynthesis by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vi7 | |||||||||||||||
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Title | Probing extradiol dioxygenase mechanism in NAD(+) biosynthesis by viewing reaction cycle intermediates - a substrate bidentately bound structure | |||||||||||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenaseHAAO | |||||||||||||||
Keywords | OXIDOREDUCTASE / In crystallo reaction / Extradiol dioxygenase / NAD+ biosynthesis / Intermediate | |||||||||||||||
Function / homology | Function and homology information 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 Similarity search - Function | |||||||||||||||
Biological species | Cupriavidus metallidurans (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.617 Å | |||||||||||||||
Authors | Wang, Y. / Liu, F. / Yang, Y. / Liu, A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vi7.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vi7.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6vi7 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vi7 | HTTPS FTP |
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-Related structure data
Related structure data | 6vi5C 6vi6C 6vi8C 6vi9C 6viaC 6vibC 6x11C 1yfuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria) Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: nbaC, Rmet_5193 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||||||
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#2: Chemical | ChemComp-3HA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / 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: 2.61→50 Å / Num. obs: 7721 / % possible obs: 99.7 % / Redundancy: 25.5 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.045 / Rrim(I) all: 0.226 / Χ2: 1.365 / Net I/σ(I): 4.3 / Num. measured all: 196633 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YFU Resolution: 2.617→37.955 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.21 Å2 / Biso mean: 21.9238 Å2 / Biso min: 1.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.617→37.955 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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