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Yorodumi- PDB-6o65: Crystal Structure of Arabidopsis thaliana Spermidine Synthase iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o65 | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine | ||||||
Components | Spermidine synthase 1 | ||||||
Keywords | TRANSFERASE / Polyamine metabolism / Putrescine Biosynthesis / dc-SAM / MTA | ||||||
Function / homology | Function and homology information spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sekula, B. / Dauter, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Plant Sci / Year: 2019 Title: Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms FromArabidopsis thaliana. Authors: Sekula, B. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o65.cif.gz | 918.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o65.ent.gz | 757.7 KB | Display | PDB format |
PDBx/mmJSON format | 6o65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o65 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o65 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 33292.957 Da / Num. of mol.: 8 / Fragment: residues 34-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SPDSYN1, At1g23820, F5O8.38 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZUB3, spermidine synthase |
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-Non-polymers , 6 types, 2127 molecules
#2: Chemical | ChemComp-S4M / #3: Chemical | ChemComp-HAI / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.18 M ammonium sulfate, 0.09 M BIS-TRIS, 22% PEG 3350, cryoprotection 25% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2019 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.6 Å / Num. obs: 200872 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10041 / CC1/2: 0.833 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.6 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.636 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.225 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.6 Å
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Refine LS restraints |
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