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Yorodumi- PDB-5kj5: Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kj5 | ||||||
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Title | Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in complex with NAD+ | ||||||
Components | 2-aminomuconate 6-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 2-aminomuconate 6-semialdehyde dehydrogenase / kynurenine pathway | ||||||
Function / homology | Function and homology information polyamine catabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å | ||||||
Authors | Yang, Y. / Davis, I. / Ha, U. / Wang, Y. / Shin, I. / Liu, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kj5.cif.gz | 390.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kj5.ent.gz | 317.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kj5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5kj5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5kj5_validation.xml.gz | 75.4 KB | Display | |
Data in CIF | 5kj5_validation.cif.gz | 105.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kj5 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kj5 | HTTPS FTP |
-Related structure data
Related structure data | 5klkC 5kllC 5klmC 5klnC 5kloC 4i26S 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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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.) Pseudomonas fluorescens (bacteria) / Gene: nbaE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83V33 #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.53 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 14, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→50 Å / Num. obs: 125557 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/av σ(I): 27.75 / Net I/σ(I): 5.9 / Num. measured all: 1782869 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I26 Resolution: 2.113→31.85 Å / FOM work R set: 0.8196 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.244 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.34 Å2 / Biso mean: 44.81 Å2 / Biso min: 23.53 Å2
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Refinement step | Cycle: final / Resolution: 2.113→31.85 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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