+Open data
-Basic information
Entry | Database: PDB / ID: 5a9r | ||||||
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Title | Apo form of Imine reductase from Amycolatopsis orientalis | ||||||
Components | IMINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / IMINE REDUCTASE / NADPH / AMINE | ||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase activity / methylated histone binding / NADP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Man, H. / Aleku, G. / Turner, N.J. / Grogan, G. | ||||||
Citation | Journal: Acs Catalysis / Year: 2016 Title: Stereoselectivity and Structural Characterization of an Imine Reductase (Ired) from Amycolatopsis Orientalis Authors: Aleku, G.A. / Man, H. / France, S.P. / Leipold, F. / Hussain, S. / Toca-Gonzalez, L. / Marchington, R. / Hart, S. / Turkenburg, J.P. / 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 | 5a9r.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a9r.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 5a9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a9r_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 5a9r_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 5a9r_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5a9r_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a9r ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a9r | HTTPS FTP |
-Related structure data
Related structure data | 5a9tC 5fwnC 3zgyS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30490.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4SNK4, EC: 1.5.1.48 |
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#2: Chemical | ChemComp-ACT / |
#3: 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M CALCIUM ACETATE, 0.1 M TRIS PH 9.0, 8% (W/V) PEG 550 MME, 8% (W/V) PEG 20K WITH PROTEIN AT A CONCENTRATION OF 20 MG PER ML |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→57.78 Å / Num. obs: 44372 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZGY Resolution: 1.55→57.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.55 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 / 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: 25.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→57.78 Å
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Refine LS restraints |
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