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- PDB-5klm: Crystal structure of 2-hydroxymuconate-6-semialdehyde derived int... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5klm | ||||||
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Title | Crystal structure of 2-hydroxymuconate-6-semialdehyde derived intermediate in NAD(+)-bound 2-aminomuconate 6-semialdehyde dehydrogenase N169D | ||||||
![]() | 2-aminomuconate 6-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / 2-aminomuconate 6-semialdehyde dehydrogenase / kynurenine pathway | ||||||
Function / homology | ![]() polyamine catabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Y. / Davis, I. / Ha, U. / Wang, Y. / Shin, I. / Liu, A. | ||||||
![]() | ![]() Title: A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism. Authors: Yang, Y. / Davis, I. / Ha, U. / Wang, Y. / Shin, I. / 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 | ![]() | 393.3 KB | Display | ![]() |
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PDB format | ![]() | 319 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 74.8 KB | Display | |
Data in CIF | ![]() | 105.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kj5C ![]() 5klkC ![]() 5kllC ![]() 5klnC ![]() 5kloC ![]() 4i26S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 56148.027 Da / Num. of mol.: 4 / Mutation: N169D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.08 M Na2HPO4 pH 9.1, 14% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 25, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 124700 / % possible obs: 99.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 42.77 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.046 / Rrim(I) all: 0.121 / Χ2: 1.047 / Net I/av σ(I): 20.206 / Net I/σ(I): 5.1 / Num. measured all: 989770 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I26 Resolution: 2.102→45.617 Å / FOM work R set: 0.827 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.576 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.51 Å2 / Biso mean: 46.13 Å2 / Biso min: 27 Å2
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Refinement step | Cycle: final / Resolution: 2.102→45.617 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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