+Open data
-Basic information
Entry | Database: PDB / ID: 7a3w | ||||||
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Title | Structure of Imine Reductase from Pseudomonas sp. | ||||||
Components | NAD(P)-dependent oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Imine / enimine / NADPH | ||||||
Function / homology | Chem-NDP Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Cuetos, A. / Thorpe, T. / Turner, N.J. / Grogan, G. | ||||||
Citation | Journal: Nature / Year: 2022 Title: Multifunctional biocatalyst for conjugate reduction and reductive amination. Authors: Thorpe, T.W. / Marshall, J.R. / Harawa, V. / Ruscoe, R.E. / Cuetos, A. / Finnigan, J.D. / Angelastro, A. / Heath, R.S. / Parmeggiani, F. / Charnock, S.J. / Howard, R.M. / Kumar, R. / ...Authors: Thorpe, T.W. / Marshall, J.R. / Harawa, V. / Ruscoe, R.E. / Cuetos, A. / Finnigan, J.D. / Angelastro, A. / Heath, R.S. / Parmeggiani, F. / Charnock, S.J. / Howard, R.M. / Kumar, R. / Daniels, D.S.B. / Grogan, G. / Turner, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a3w.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a3w.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 7a3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/7a3w ftp://data.pdbj.org/pub/pdb/validation_reports/a3/7a3w | HTTPS FTP |
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-Related structure data
Related structure data | 6eodS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 0 / Auth seq-ID: 7 - 293 / Label seq-ID: 7 - 293
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-Components
#1: Protein | Mass: 31105.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: HGP31_19350 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris buffer pH 6.5, 25% (w/v) PEG (polyethylene glycol) 3350 and 5 mM NADP+. |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→81.85 Å / Num. obs: 57157 / % possible obs: 83 % / Redundancy: 4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.59→1.62 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3245 / CC1/2: 0.85 / Rpim(I) all: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EOD Resolution: 1.59→81.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.15 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 58.87 Å2 / Biso mean: 20.877 Å2 / Biso min: 11.62 Å2
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Refinement step | Cycle: final / Resolution: 1.59→81.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9001 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.59→1.631 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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