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- PDB-4hsj: 1.88 angstrom x-ray crystal structure of piconlinic-bound 3-hydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hsj | ||||||
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Title | 1.88 angstrom x-ray crystal structure of piconlinic-bound 3-hydroxyanthranilate-3,4-dioxygenase | ||||||
![]() | 3-hydroxyanthranilate 3,4-dioxygenase | ||||||
![]() | Oxidoreductase/Oxidoreductase inhibitor / bi-cupin / dioxygenase / OXIDOREDUCTASE / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, F. / Chen, L. / Davis, C.I. / Liu, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.5 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hvoC ![]() 4hvqC ![]() 4l2nC ![]() 1yfuS ![]() 4hsk ![]() 4hsm S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-6PC / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.88 % |
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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: ![]() ![]() ![]() |
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: 1.88→50 Å / Num. all: 20174 / Num. obs: 19992 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.3 % / Rsym value: 0.065 / Net I/σ(I): 78.88 |
Reflection shell | Resolution: 1.88→1.91 Å / % possible all: 90.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YFU Resolution: 1.883→30.667 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.58 / 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: 35.394 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.17 Å2 / Biso mean: 28.7514 Å2 / Biso min: 14.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.883→30.667 Å
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Refine LS restraints |
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