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Yorodumi- PDB-3zgy: Apo-structure of R-selective imine reductase from Streptomyces ka... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zgy | ||||||
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Title | Apo-structure of R-selective imine reductase from Streptomyces kanamyceticus | ||||||
Components | R-IMINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES KANAMYCETICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Rodriguez Mata, M. / Frank, A. / Grogan, G. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Structure and Activity of Nadph-Dependent Reductase Q1Eqe0 from Streptomyces Kanamyceticus, which Catalyses the R-Selective Reduction of an Imine Substrate. Authors: Rodriguez Mata, M. / Frank, A. / Wells, E. / Leipold, F. / Turner, N.J. / Hart, S. / Turknburg, J.P. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zgy.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zgy.ent.gz | 165.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/3zgy ftp://data.pdbj.org/pub/pdb/validation_reports/zg/3zgy | HTTPS FTP |
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-Related structure data
Related structure data | 3zhbC 1yb4S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31545.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES KANAMYCETICUS (bacteria) / Strain: 12-6 / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1EQE0, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor #2: 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: 4 Å3/Da / Density % sol: 69.3 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN AT 10 MG ML-1. 35% (V/V) TASCIMATE PH 7.0 WITH 2.5% (V/V) ETHYLENE GLYCOL. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→108.68 Å / Num. obs: 49759 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.71→2.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YB4 Resolution: 2.71→36.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.58 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.238 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.619 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→36.23 Å
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Refine LS restraints |
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