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Yorodumi- PDB-6cd3: Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cd3 | ||||||||||||
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Title | Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A from Cupriavidus metallidurans in complex with 3-HAA | ||||||||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenaseHAAO | ||||||||||||
Keywords | OXIDOREDUCTASE / Holo structure / Dioxygenase / Mutant I142A | ||||||||||||
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: 2.612 Å | ||||||||||||
Authors | Yang, Y. / Liu, F. / Liu, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J. Biol. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cd3.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cd3.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 6cd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd3 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd3 | HTTPS FTP |
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-Related structure data
Related structure data | 6bvpC 6bvqC 6bvrC 6bvsC 6d60C 6d61C 6d62C 4l2nS 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: 22548.297 Da / Num. of mol.: 1 / Mutation: I142A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / 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 | #3: Chemical | ChemComp-3HA / | #4: 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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000 13%, 0.1 M Tris-HCl, 0.2 M MgCl2, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 7693 / % possible obs: 98.4 % / Redundancy: 15.2 % / Biso Wilson estimate: 32.52 Å2 / Rmerge(I) obs: 0.178 / Χ2: 1.031 / Net I/σ(I): 5.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L2N Resolution: 2.612→25.062 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.7 Å2 / Biso mean: 31.1942 Å2 / Biso min: 15.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.612→25.062 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: 5
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