+Open data
-Basic information
Entry | Database: PDB / ID: 6g1m | ||||||
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Title | Amine Dehydrogenase from Petrotoga mobilis; open and closed form | ||||||
Components | Dihydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / Amine Dehydrogenase / reductive aminase / NADH | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate reductase / lysine biosynthetic process via diaminopimelate Similarity search - Function | ||||||
Biological species | Petrotoga mobilis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Beloti, L. / Frese, A. / Mayol, O. / Vaxelaire-Vergne, 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. / Vaxelaire-Vergne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g1m.cif.gz | 262.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1m.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 6g1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g1m_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6g1m_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6g1m_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 6g1m_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1m ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1m | HTTPS FTP |
-Related structure data
Related structure data | 6g1hSC 6iaqC 6iauC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335
NCS ensembles :
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-Components
#1: Protein | Mass: 36844.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petrotoga mobilis (strain DSM 10674 / SJ95) (bacteria) Strain: DSM 10674 / SJ95 / Gene: Pmob_1166 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BHL2 #2: Chemical | ChemComp-NAD / #3: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 6.5, 0,2M Li2SO4, 25% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97965 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97965 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→125.36 Å / Num. obs: 62492 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.32→2.38 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4560 / CC1/2: 0.82 / Rpim(I) all: 0.43 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G1H Resolution: 2.32→125.36 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.088 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.29 / 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: 33.936 Å2
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Refinement step | Cycle: 1 / Resolution: 2.32→125.36 Å
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Refine LS restraints |
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