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- PDB-6sep: Crystal Structure of the Homospermidine Synthase (HSS) variant W2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sep | ||||||
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Title | Crystal Structure of the Homospermidine Synthase (HSS) variant W229E from Blastochloris viridis in Complex with NAD | ||||||
![]() | Homospermidine synthase | ||||||
![]() | TRANSFERASE / Homospermidine Synthase / Rossmann Fold / NAD / Putrescine | ||||||
Function / homology | ![]() homospermidine synthase (spermidine-specific) activity / homospermidine synthase / homospermidine synthase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Helfrich, F. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction. Authors: Helfrich, F. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 392.3 KB | Display | ![]() |
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PDB format | ![]() | 302.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s3xC ![]() 6s49C ![]() 6s4dC ![]() 6s6gC ![]() 6s72C ![]() 6y87C ![]() 4plpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 52980.395 Da / Num. of mol.: 2 / Mutation: W229E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: Sodium acetate, Ammonium acetate, PEG 10000, NDSB-201, Agmatine sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→109.86 Å / Num. obs: 85769 / % possible obs: 98.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 18.69 Å2 / Rrim(I) all: 1.23381 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 1.87→1.91 Å / Num. unique obs: 3354 / Rrim(I) all: 0.77686 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PLP Resolution: 2.2→90.31 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5722
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→90.31 Å
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Refine LS restraints |
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LS refinement shell |
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