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Yorodumi- PDB-4l2n: Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l2n | ||||||
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Title | Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Catalytic Intermediates - ligand-free structure | ||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / bi-cupin iron-binding / dioxygenase | ||||||
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: 1.74 Å | ||||||
Authors | Liu, F. / Liu, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. Authors: Liu, F. / Geng, J. / Gumpper, R.H. / Barman, A. / Davis, I. / Ozarowski, A. / Hamelberg, D. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l2n.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l2n.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 4l2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l2n_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 4l2n_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 4l2n_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4l2n_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l2n ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l2n | HTTPS FTP |
-Related structure data
Related structure data | 4hsjC 4hvoC 4hvqC 1yfuS 4l2p 4l2q 4l2r 4l2s 4l2t 4l2u 4l2v 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20056.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: Cupriavidus metallidurans, nbaC, Rmet_5193 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DH5 alpha) References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, 0.1M Tris-HCl, 200 mM MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. all: 25017 / Num. obs: 24242 / % possible obs: 96.9 % / Observed criterion σ(F): 0 |
Reflection shell | Resolution: 1.75→1.78 Å / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFU Resolution: 1.74→34.129 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.94 Å2 / ksol: 0.403 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.41 Å2 / Biso mean: 32.4994 Å2 / Biso min: 17.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→34.129 Å
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Refine LS restraints |
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