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- PDB-7ui3: Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ui3 | |||||||||
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Title | Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding | |||||||||
![]() | Tryptophan 2,3-dioxygenase![]() | |||||||||
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Function / homology | ![]() response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yeh, S.-R. / Geeraerts, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding Authors: Yeh, S.-R. / Geeraerts, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.8 KB | Display | ![]() |
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PDB format | ![]() | 355 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pyzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 45182.535 Da / Num. of mol.: 4 / Fragment: UNP residues 18-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZIQ / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow![]() | Temperature: 293 K / Method: microbatch / pH: 5.6 Details: 50 mM Sodium Citrate, pH 5.6 2% Tacsimate PEG 3350 (4-12%) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2021 Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection | Resolution: 3.18→19.974 Å / Num. obs: 34269 / % possible obs: 99.5 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Net I/σ(I): 18.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6PYZ Resolution: 3.18→19.974 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.227 / SU B: 28.651 / SU ML: 0.452 / Average fsc free: 0.8269 / Average fsc work: 0.8441 / Cross valid method: FREE R-VALUE / ESU R Free: 0.479 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.154 Å2
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Refinement step | Cycle: LAST / Resolution: 3.18→19.974 Å
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Refine LS restraints |
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LS refinement shell |
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