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Yorodumi- PDB-6s3x: Crystal Structure of the Homospermidine Synthase (HSS) variant E2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3x | |||||||||
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Title | Crystal Structure of the Homospermidine Synthase (HSS) variant E210Q 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 / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | Blastochloris viridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 | 6s3x.cif.gz | 376.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3x.ent.gz | 308.8 KB | Display | PDB format |
PDBx/mmJSON format | 6s3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3x ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3x | HTTPS FTP |
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-Related structure data
Related structure data | 6s49C 6s4dC 6s6gC 6s72C 6sepC 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
#1: Protein | Mass: 53036.508 Da / Num. of mol.: 2 / Mutation: E210Q 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 | #5: 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: 2.5 Å3/Da / Density % sol: 50.84 % |
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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: P14 (MX2) / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→90.36 Å / Num. obs: 111532 / % possible obs: 89.5 % / Redundancy: 7 % / Rrim(I) all: 0.197 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.66→1.69 Å / Num. unique obs: 1004 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PLP Resolution: 1.72→90.36 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→90.36 Å
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Refine LS restraints |
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LS refinement shell |
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