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Yorodumi- PDB-6sep: Crystal Structure of the Homospermidine Synthase (HSS) variant W2... -
+Open data
-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 | ||||||
Components | Homospermidine synthase | ||||||
Keywords | TRANSFERASE / Homospermidine Synthase / Rossmann Fold / NAD / Putrescine | ||||||
Function / homology | Function and homology information homospermidine synthase (spermidine-specific) activity / homospermidine synthase / homospermidine synthase activity Similarity search - Function | ||||||
Biological species | Blastochloris viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Helfrich, F. / Scheidig, A.J. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sep.cif.gz | 392.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sep.ent.gz | 302.4 KB | Display | PDB format |
PDBx/mmJSON format | 6sep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6sep ftp://data.pdbj.org/pub/pdb/validation_reports/se/6sep | HTTPS FTP |
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-Related structure data
Related structure data | 6s3xC 6s49C 6s4dC 6s6gC 6s72C 6y87C 4plpS 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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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.) Blastochloris viridis (bacteria) / Gene: hss / Production host: Escherichia coli (E. coli) / References: UniProt: O32323, homospermidine synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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