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Yorodumi- PDB-6jnk: Crystal structure of Azospirillum brasilense L-arabinose 1-dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jnk | ||||||
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Title | Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (NADP-bound form) | ||||||
Components | L-arabinose 1-dehydrogenase (NAD(P)(+)) | ||||||
Keywords | OXIDOREDUCTASE / L-arabinose metabolism / NADP-dependent dehydrogenase / Gfo/Idh/MocA protein family | ||||||
Function / homology | Function and homology information 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 / NADP+ binding ...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 / NADP+ binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding Similarity search - Function | ||||||
Biological species | Azospirillum brasilense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Watanabe, Y. / Iga, C. / Watanabe, S. | ||||||
Citation | Journal: Febs Lett. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jnk.cif.gz | 256.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jnk.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/6jnk ftp://data.pdbj.org/pub/pdb/validation_reports/jn/6jnk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33861.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q53TZ2, L-arabinose 1-dehydrogenase [NAD(P)+], galactose 1-dehydrogenase (NADP+), D-galactose 1-dehydrogenase #2: Chemical | ChemComp-NAP / #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: 2.61 Å3/Da / Density % sol: 52.96 % 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 / pH: 8.5 / Details: 25% PEG 3350, 0.1 M Tris-HCl pH 8.5, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 68572 / % possible obs: 99.1 % / Redundancy: 3.53 % / CC1/2: 0.992 / Rrim(I) all: 0.155 / Rsym value: 0.131 / Net I/σ(I): 6.26 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.62 % / Num. unique obs: 22054 / Rrim(I) all: 1.015 / Rsym value: 0.865 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.636 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.71 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.89 Å2 / Biso mean: 39.0114 Å2 / Biso min: 18.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→46.636 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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