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- PDB-6jnj: Crystal structure of Azospirillum brasilense L-arabinose 1-dehydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jnj | ||||||
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Title | Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form) | ||||||
![]() | L-arabinose 1-dehydrogenase (NAD(P)(+)) | ||||||
![]() | OXIDOREDUCTASE / L-arabinose metabolism / NADP-dependent dehydrogenase / Gfo/Idh/MocA protein family | ||||||
Function / homology | ![]() L-arabinose 1-dehydrogenase [NAD(P)+] / L-arabinose catabolic process / L-arabinose 1-dehydrogenase (NADP+) activity / L-arabinose 1-dehydrogenase (NAD+) activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / L-arabinose catabolic process to 2-oxoglutarate / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...L-arabinose 1-dehydrogenase [NAD(P)+] / L-arabinose catabolic process / L-arabinose 1-dehydrogenase (NADP+) activity / L-arabinose 1-dehydrogenase (NAD+) activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / L-arabinose catabolic process to 2-oxoglutarate / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP+ binding / NAD+ binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, Y. / Iga, C. / Watanabe, S. | ||||||
![]() | ![]() Title: Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase. Authors: Watanabe, Y. / Iga, C. / Watanabe, Y. / Watanabe, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147 KB | Display | ![]() |
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PDB format | ![]() | 112.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jnkC ![]() 4ew6S 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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Unit cell |
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Components
#1: Protein | Mass: 33992.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q53TZ2, L-arabinose 1-dehydrogenase [NAD(P)+], galactose 1-dehydrogenase (NADP+), D-galactose 1-dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 115047 / % possible obs: 98.8 % / Redundancy: 3.3 % / Net I/σ(I): 5.47 |
Reflection shell | Resolution: 1.5→1.54 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EW6 Resolution: 1.5→46.457 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 22.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.09 Å2 / Biso mean: 21.3138 Å2 / Biso min: 9.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→46.457 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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