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Yorodumi- PDB-4i3p: 1.96 angstrom x-ray crystal structure of 3-hydroxyanthranilate-3,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i3p | ||||||
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Title | 1.96 angstrom x-ray crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase bound with 3-aminosalicylic acid from cupriavidus metallidurans | ||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenaseHAAO | ||||||
Keywords | Oxioreductase/substrate / bi-cupin iron-binding / dioxygenase / Oxioreductase-substrate complex | ||||||
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: 1.961 Å | ||||||
Authors | Liu, F. / Liu, A. | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.96 angstrom x-ray crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase bound with 3-aminosalicylic acid from cupraavidus metallidurans Authors: 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 | 4i3p.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i3p.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 4i3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/4i3p ftp://data.pdbj.org/pub/pdb/validation_reports/i3/4i3p | HTTPS FTP |
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-Related structure data
Related structure data | 1yfuS S: Starting model for refinement |
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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 on special symmetry positions |
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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-1CW / | #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: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 8000, 0.1M Tris-HCL, pH 9.0, 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. all: 17980 / Num. obs: 16434 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→1.98 Å / % possible all: 71.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1yfu Resolution: 1.961→34.243 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 29.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.234 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.63 Å2 / Biso mean: 40.0385 Å2 / Biso min: 22.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.961→34.243 Å
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Refine LS restraints | Type: f_bond_refined_d / Dev ideal: 0.008 |