+Open data
-Basic information
Entry | Database: PDB / ID: 6g1h | ||||||
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Title | Amine Dehydrogenase from Petrotoga mobilis; open form | ||||||
Components | Dihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / amine dehydrogenase / reductive aminase / NADH | ||||||
Function / homology | 2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / 4-hydroxy-tetrahydrodipicolinate reductase / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / lysine biosynthetic process via diaminopimelate / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrodipicolinate reductase Function and homology information | ||||||
Biological species | Petrotoga mobilis SJ95 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | ||||||
Authors | Beloti, L. / Frese, A. / Mayol, O. / Vergne-Vaxelaire, C. / Grogan, G. | ||||||
Citation | Journal: Nat Catal / Year: 2019 Title: A family of native amine dehydrogenases for the asymmetric reductive amination of ketones Authors: Mayol, O. / Bastard, K. / Beloti, L. / Frese, A. / Turkenburg, J.P. / Petit, J.-L. / Mariage, A. / Debard, A. / Pellouin, V. / Perret, A. / de Berardinis, V. / Zaparucha, A. / Grogan, G. / Vergne-Vaxelaire, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g1h.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1h.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1h ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1h | HTTPS FTP |
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-Related 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: 37644.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petrotoga mobilis SJ95 (bacteria) / Gene: Pmob_1166 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BHL2 | ||
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#2: Chemical | ChemComp-NAD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-tris pH 6.5 0.8M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→71.04 Å / Num. obs: 41623 / % possible obs: 99.2 % / Redundancy: 23.6 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.79→1.83 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2379 / CC1/2: 0.99 / Rpim(I) all: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→71.04 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.054 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.099 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.508 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→71.04 Å
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Refine LS restraints |
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