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Yorodumi- PDB-7cgr: Crystal structure of Azospirillum brasilense L-arabinose 1-dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cgr | ||||||
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Title | Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase E147A mutant (NADP and glycerol 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 / 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 | Azospirillum brasilense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å | ||||||
Authors | Yoshiwara, K. / Watanabe, Y. / Watanabe, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of bacterial L-arabinose 1-dehydrogenase in complex with L-arabinose and NADP+ Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cgr.cif.gz | 263.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cgr.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 7cgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cgr_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7cgr_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7cgr_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 7cgr_validation.cif.gz | 74.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/7cgr ftp://data.pdbj.org/pub/pdb/validation_reports/cg/7cgr | HTTPS FTP |
-Related structure data
Related structure data | 7cgqC 6jnkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34967.727 Da / Num. of mol.: 4 / Mutation: E147A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araA / Production host: Escherichia coli (E. coli) References: UniProt: Q53TZ2, L-arabinose 1-dehydrogenase [NAD(P)+], galactose 1-dehydrogenase (NADP+), D-galactose 1-dehydrogenase #2: Chemical | ChemComp-NAP / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.55 Å3/Da / Density % sol: 51.81 % 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: 0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.09→49.171 Å / Num. obs: 82746 / % possible obs: 99.6 % / Redundancy: 3.448 % / Biso Wilson estimate: 35.093 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.176 / Χ2: 0.796 / Net I/σ(I): 7.09 / Num. measured all: 559968 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JNK Resolution: 2.093→48.934 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML 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 / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.98 Å2 / Biso mean: 32.0001 Å2 / Biso min: 14.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.093→48.934 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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