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Yorodumi- PDB-6via: Observing a ring-cleaving dioxygenase in action through a crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6via | |||||||||||||||
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Title | Observing a ring-cleaving dioxygenase in action through a crystalline lens - a seven-membered lactone bound structure | |||||||||||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenase | |||||||||||||||
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 / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Cupriavidus metallidurans (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 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 | 6via.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6via.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 6via.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6via_validation.pdf.gz | 345.4 KB | Display | wwPDB validaton report |
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Full document | 6via_full_validation.pdf.gz | 345.4 KB | Display | |
Data in XML | 6via_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6via_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6via ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6via | HTTPS FTP |
-Related structure data
Related structure data | 6vi5C 6vi6C 6vi7C 6vi8C 6vi9C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 6 types, 179 molecules
#2: Chemical | #3: Chemical | ChemComp-FE2 / | #4: Chemical | ChemComp-FE / | #5: Chemical | ChemComp-OH / | #6: Chemical | ChemComp-EAY / ( | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Nonpolymer details | Ligand EAY is an intermediate. This intermediate is thought to be a epsylon-lactone radical (on C11) ...Ligand EAY is an intermediate. This intermediate is thought to be a epsylon-lactone radical (on C11) with an Fe(III)-bound hydroxide or its resonance structure composed by a neutral epsylon-lactone (C11 and O12 form double bond) with an Fe(II)-bound hydroxide |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% 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-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→50 Å / Num. obs: 32318 / % possible obs: 98.2 % / Redundancy: 31.2 % / Biso Wilson estimate: 25.63 Å2 / Rmerge(I) obs: 0.083 / Χ2: 0.991 / Net I/σ(I): 5.9 / Num. measured all: 1009118 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.591→30.732 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.76 / 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: 109.68 Å2 / Biso mean: 41.9275 Å2 / Biso min: 20.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.591→30.732 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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Refinement TLS params. | Method: refined / Origin x: -10.1576 Å / Origin y: -24.0878 Å / Origin z: 4.8173 Å
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Refinement TLS group |
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