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Yorodumi- PDB-7bxr: 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bxr | |||||||||
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Title | 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form | |||||||||
Components | 2-amino-3-ketobutyrate coenzyme A ligase | |||||||||
Keywords | LIGASE / TRANSFERASE / 2-amino-3-ketobutyrate CoA ligase / Cupriavidus necator | |||||||||
Function / homology | Function and homology information glycine C-acetyltransferase / glycine C-acetyltransferase activity / L-threonine catabolic process to glycine / biosynthetic process / ligase activity / pyridoxal phosphate binding / cytosol Similarity search - Function | |||||||||
Biological species | Cupriavidus necator (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Motoyama, T. / Nakano, S. / Hasebe, F. / Miyoshi, N. / Ito, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Commun Chem / Year: 2021 Title: Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Authors: Motoyama, T. / Nakano, S. / Hasebe, F. / Miyata, R. / Kumazawa, S. / Miyoshi, N. / Ito, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bxr.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bxr.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bxr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7bxr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7bxr_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 7bxr_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/7bxr ftp://data.pdbj.org/pub/pdb/validation_reports/bx/7bxr | HTTPS FTP |
-Related structure data
Related structure data | 7bxpC 7bxqC 7bxsC 1fc4S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44791.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: kbl, H16_B0819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0K313, glycine C-acetyltransferase #2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3350, 3% w/v D-Sorbitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→47.8 Å / Num. obs: 24744 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.4 Å2 / CC1/2: 0.996 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.55→2.64 Å / Num. unique obs: 3571 / CC1/2: 0.856 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FC4 Resolution: 2.55→47.76 Å / SU ML: 0.3495 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.653 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 36.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→47.76 Å
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Refine LS restraints |
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LS refinement shell |
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