+Open data
-Basic information
Entry | Database: PDB / ID: 8gxd | |||||||||
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Title | L-LEUCINE DEHYDROGENASE FROM EXIGUOBACTERIUM SIBIRICUM | |||||||||
Components | Glu/Leu/Phe/Val dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / L-LEUCINE DEHYDROGENASE | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | Exiguobacterium sibiricum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | |||||||||
Authors | Mu, X. / Nie, Y. / Wu, T. / Wang, Y. / Zhang, N. / Yin, D. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: Reshaping Substrate-Binding Pocket of Leucine Dehydrogenase for Bidirectionally Accessing Structurally Diverse Substrates Authors: Wu, T. / Wang, Y. / Zhang, N. / Yin, D. / Xu, Y. / Nie, Y. / Mu, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gxd.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gxd.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gxd_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 8gxd_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 8gxd_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 8gxd_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/8gxd ftp://data.pdbj.org/pub/pdb/validation_reports/gx/8gxd | HTTPS FTP |
-Related structure data
Related structure data | 6acfS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40600.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15) (bacteria) Gene: Exig_0916 / Production host: Escherichia coli (E. coli) / References: UniProt: B1YLR3, EC: 1.4.1.9 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.76 Å3/Da / Density % sol: 74.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M calcium chloride, 0.1M sodium acetate buffer (pH 4.6), 20% glycerol (w/v) |
-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: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→47.62 Å / Num. obs: 15638 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.986 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.02→3.2 Å / Num. unique obs: 2418 / CC1/2: 0.699 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ACF Resolution: 3.02→47.62 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.871 / SU B: 15.959 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.38 Å2 / Biso mean: 45.146 Å2 / Biso min: 8.18 Å2
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Refinement step | Cycle: final / Resolution: 3.02→47.62 Å
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LS refinement shell | Resolution: 3.02→3.095 Å / Rfactor Rfree error: 0
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