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Yorodumi- PDB-6rl5: The first crystal structure of the DABA aminotransferase EctB in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rl5 | ||||||
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Title | The first crystal structure of the DABA aminotransferase EctB in the ectoine biosynthesis pathway of the model organism Chromohalobacter salexigens DSM 3034 | ||||||
Components | Diaminobutyrate--2-oxoglutarate transaminase | ||||||
Keywords | TRANSFERASE / Ectoine / DABA aminotransferase / osmoadaptation | ||||||
Function / homology | Function and homology information diaminobutyrate-2-oxoglutarate transaminase / diaminobutyrate-2-oxoglutarate transaminase activity / diaminobutyrate-pyruvate transaminase activity / ectoine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Chromohalobacter salexigens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Hillier, H.T. / Altermark, B. / Leiros, I. | ||||||
Citation | Journal: Febs J. / Year: 2020 Title: The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway. Authors: Hillier, H.T. / Altermark, B. / Leiros, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rl5.cif.gz | 628.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rl5.ent.gz | 520.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/6rl5 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/6rl5 | HTTPS FTP |
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-Related structure data
Related structure data | 1sf2S S: Starting model for refinement |
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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: 47086.125 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Synthetic construct containing a 6xHIS C-terminal purification tag Source: (gene. exp.) Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768) (bacteria) Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: ectB, Csal_1877 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21*(DE3) References: UniProt: Q9ZEU7, diaminobutyrate-2-oxoglutarate transaminase #2: Chemical | ChemComp-PLP / #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: 2.55 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium malonate, 0.1M BisTris propane pH 6.5, 30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2018 / Details: toroidal mirror |
Radiation | Monochromator: Si (111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→49.073 Å / Num. obs: 136967 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rpim(I) all: 0.047 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6796 / Rpim(I) all: 1.07 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1sf2 Resolution: 2.45→49.073 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→49.073 Å
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Refine LS restraints |
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LS refinement shell |
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