[English] 日本語
Yorodumi- PDB-6s6g: Crystal Structure of the Homospermidine Synthase (HSS) variant E1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s6g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Homospermidine Synthase (HSS) variant E117Q 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: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6s6g.cif.gz | 404.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s6g.ent.gz | 308.3 KB | Display | PDB format |
PDBx/mmJSON format | 6s6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s6g_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6s6g_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6s6g_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 6s6g_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/6s6g ftp://data.pdbj.org/pub/pdb/validation_reports/s6/6s6g | HTTPS FTP |
-Related structure data
Related structure data | 6s3xC 6s49C 6s4dC 6s72C 6sepC 6y87C 4plpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53036.508 Da / Num. of mol.: 2 / Mutation: E117Q, G1 -G4 expression tag 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: Chemical | #4: Chemical | ChemComp-1PS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Sodium acetate, Ammonium acetate, PEG 10000, NDSB-201, Agmatine sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: Oct 10, 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: 1.6→79.22 Å / Num. obs: 134938 / % possible obs: 96.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 21.33 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 3613 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PLP Resolution: 1.6→60.3829 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5844
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→60.3829 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|