+Open data
-Basic information
Entry | Database: PDB / ID: 8hpe | ||||||
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Title | Crystal structure of Leucine dehydrogenase | ||||||
Components | Leucine dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Leucine dehydrogenase | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Li, X. / Song, W. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: A Tri-Enzyme Cascade for Efficient Production of L-2-Aminobutyrate from L-Threonine. Authors: Li, X. / Gao, C. / Wei, W. / Song, W. / Meng, W. / Liu, J. / Chen, X. / Gao, C. / Guo, L. / Liu, L. / Wu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hpe.cif.gz | 288 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hpe.ent.gz | 237.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hpe_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 8hpe_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 8hpe_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 8hpe_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hpe ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hpe | HTTPS FTP |
-Related structure data
Related structure data | 8hr6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39865.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) Gene: ldh1, BK774_17255, BK775_32270, BTGOE4_46100, BUM91_06765, C5676_00473, D7J84_18335, GH851_02505, GH891_02550 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3E5D9, EC: 1.4.1.9 #2: Chemical | ChemComp-SO4 / #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: 4.07 Å3/Da / Density % sol: 69.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% glycerol, 1.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Dec 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→46.2 Å / Num. obs: 22022 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.302 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.22→3.48 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 4448 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→46.24 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.869 / SU B: 61.788 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.499 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.592 Å2
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Refinement step | Cycle: 1 / Resolution: 3.22→46.24 Å
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Refine LS restraints |
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