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Yorodumi- PDB-8hp3: Crystal structure of meso-diaminopimelate dehydrogenase from Prev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hp3 | ||||||
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Title | Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis | ||||||
Components | Meso-diaminopimelate D-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / C2221 / 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: 3.07 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 | 8hp3.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hp3.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hp3_validation.pdf.gz | 4.8 MB | Display | wwPDB validaton report |
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Full document | 8hp3_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 8hp3_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 8hp3_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hp3 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hp3 | HTTPS FTP |
-Related structure data
Related structure data | 8hp0C 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: Chemical | ChemComp-EDO / #5: 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: 51.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 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: Nov 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→47.53 Å / Num. obs: 18754 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.07→3.28 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 3351 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→47.53 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 24.307 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / 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: 52.028 Å2
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Refinement step | Cycle: 1 / Resolution: 3.07→47.53 Å
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Refine LS restraints |
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