+Open data
-Basic information
Entry | Database: PDB / ID: 5gz3 | ||||||
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Title | Structure of D-amino acid dehydrogenase in complex with NADP | ||||||
Components | Meso-diaminopimelate D-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate Similarity search - Function | ||||||
Biological species | Ureibacillus thermosphaericus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Sakuraba, H. / Seto, T. / Hayashi, J. / Akita, H. / Yoneda, K. / Ohshima, T. | ||||||
Citation | Journal: Appl. Environ. Microbiol. / Year: 2017 Title: Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase Authors: Hayashi, J. / Seto, T. / Akita, H. / Watanabe, M. / Hoshino, T. / Yoneda, K. / Ohshima, T. / Sakuraba, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gz3.cif.gz | 257.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gz3.ent.gz | 207.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gz3 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gz3 | HTTPS FTP |
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-Related structure data
Related structure data | 5gz1SC 5gz6C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35881.441 Da / Num. of mol.: 2 Mutation: Q154L, D158G, T173I, R199M, H249N, D94A, and Y224F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ureibacillus thermosphaericus (bacteria) Gene: ddh / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3) / References: UniProt: G1UII1, diaminopimelate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46.12 % / Mosaicity: 1.231 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2015 / Details: silicon single crystal | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→50 Å / Num. obs: 81038 / % possible obs: 93.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 38.091 / Net I/σ(I): 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GZ1 Resolution: 1.59→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.759 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.6 Å2 / Biso mean: 20.81 Å2 / Biso min: 3.02 Å2
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Refinement step | Cycle: final / Resolution: 1.59→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.591→1.632 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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