+Open data
-Basic information
Entry | Database: PDB / ID: 4d3s | ||||||
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Title | Imine reductase from Nocardiopsis halophila | ||||||
Components | IMINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NADPH | ||||||
Function / homology | Function and homology information dihydrofolate reductase / dihydrofolate reductase activity / NADP binding Similarity search - Function | ||||||
Biological species | NOCARDIOPSIS HALOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: Structure, Activity and Stereoselectivity of Nadph-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline. Authors: Man, H. / Wells, E. / Hussain, S. / Leipold, F. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d3s.cif.gz | 408.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d3s.ent.gz | 332.3 KB | Display | PDB format |
PDBx/mmJSON format | 4d3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d3s_validation.pdf.gz | 855.4 KB | Display | wwPDB validaton report |
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Full document | 4d3s_full_validation.pdf.gz | 900.2 KB | Display | |
Data in XML | 4d3s_validation.xml.gz | 82.7 KB | Display | |
Data in CIF | 4d3s_validation.cif.gz | 113.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3s ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3s | HTTPS FTP |
-Related structure data
Related structure data | 4d3dC 4d3fC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 30757.660 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOCARDIOPSIS HALOPHILA (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A0J9X1X6*PLUS, dihydrofolate reductase #2: Sugar | #3: Water | ChemComp-HOH / | Nonpolymer details | N-OCTYL-BETA-D-GLUCOPYRAN | |
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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18% (W/V) PEG 3350; 0. 2 M MGCL2; 0.1M BIS-TRIS PROPANE PH 5.5; 1% (W/V) N-OCTYL-BETA-D-OCTYLPYRANOSIDE |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→67.57 Å / Num. obs: 94683 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.39→2.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZGY Resolution: 2.24→67.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.948 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.239 / 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: 48.319 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→67.57 Å
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Refine LS restraints |
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