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Yorodumi- PDB-6x11: Observing a ring-cleaving dioxygenase in action through a crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x11 | |||||||||||||||
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Title | Observing a ring-cleaving dioxygenase in action through a crystalline lens - an enol tautomer of ACMS monodentately 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: 2.097 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 | 6x11.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x11.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 6x11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/6x11 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/6x11 | HTTPS FTP |
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-Related structure data
Related structure data | 6vi5C 6vi6C 6vi7C 6vi8C 6vi9C 6viaC 6vibC 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 on special symmetry positions |
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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) References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||||||
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#2: Chemical | ChemComp-TRS / | ||||||
#3: Chemical | #4: Chemical | ChemComp-2FO / ( | #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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging 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: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.097→50 Å / Num. obs: 14606 / % possible obs: 98.5 % / Redundancy: 27.5 % / Biso Wilson estimate: 30.39 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.029 / Net I/σ(I): 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YFU Resolution: 2.097→38.189 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.66 Å2 / Biso mean: 35.4492 Å2 / Biso min: 16.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.097→38.189 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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