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Yorodumi- PDB-8hp0: Crystal structure of meso-diaminopimelate dehydrogenase from Prev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hp0 | ||||||
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Title | Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis | ||||||
Components | Meso-diaminopimelate D-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / asymmetric unit / C221 / fold | ||||||
Function / homology | Function and homology information diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotide binding Similarity search - Function | ||||||
Biological species | Prevotella timonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Tan, Y. / Song, W. | ||||||
Funding support | 1items
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Citation | Journal: Appl.Environ.Microbiol. / Year: 2023 Title: Rational Design of Meso -Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d- p -Hydroxyphenylglycine. Authors: Tan, Y. / Gao, C. / Song, W. / Wei, W. / Liu, J. / Gao, C. / Guo, L. / Chen, X. / 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 | 8hp0.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hp0.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hp0_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 8hp0_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 8hp0_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 8hp0_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hp0 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hp0 | HTTPS FTP |
-Related structure data
Related structure data | 8hp3C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 32584.482 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prevotella timonensis (bacteria) / Gene: BFS16_11360 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2K0XCZ3, diaminopimelate dehydrogenase #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: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, and 0.1 M 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: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Feb 28, 2022 / Details: multilayer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→44.87 Å / Num. obs: 35517 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.47→2.57 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.507 / Num. unique obs: 3948 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→44.91 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.393 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.638 / ESU R Free: 0.305 / 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: 41.692 Å2
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Refinement step | Cycle: 1 / Resolution: 2.47→44.91 Å
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Refine LS restraints |
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