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Yorodumi- PDB-8hr6: leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hr6 | ||||||
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Title | leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis | ||||||
Components | Leucine dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis | ||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.52 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 | 8hr6.cif.gz | 286.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hr6.ent.gz | 236.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hr6_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8hr6_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 8hr6_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8hr6_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hr6 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hr6 | HTTPS FTP |
-Related structure data
Related structure data | 8hpeC 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 | #3: Chemical | ChemComp-SO4 / #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: 4.13 Å3/Da / Density % sol: 70.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% glycerol, 3.75% isopropanol, 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 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Mar 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.52→30.79 Å / Num. obs: 17215 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.995 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.52→3.85 Å / Num. unique obs: 4016 / CC1/2: 0.948 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→30.79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 63.832 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / 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: 78.61 Å2
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Refinement step | Cycle: 1 / Resolution: 3.52→30.79 Å
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