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Yorodumi- PDB-6o64: Crystal Structure of Arabidopsis thaliana Spermidine Synthase iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o64 | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2) | ||||||
Components | Spermidine synthase 2 | ||||||
Keywords | TRANSFERASE / Polyamine metabolism / Putrescine Biosynthesis / dc-SAM / MTA | ||||||
Function / homology | Function and homology information spermidine synthase / spermidine synthase activity / polyamine biosynthetic process / spermidine biosynthetic process / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6o64.cif.gz | 872.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o64.ent.gz | 730 KB | Display | PDB format |
PDBx/mmJSON format | 6o64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o64 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o64 | 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: 33456.125 Da / Num. of mol.: 8 / Fragment: residues 39-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SPDSYN2, At1g70310, F17O7.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O48661, spermidine synthase |
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-Non-polymers , 6 types, 959 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-MLI / #6: Chemical | ChemComp-EDO / | #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: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus screen G4 (Carboxylic acids, buffer system 1, precipitant mix 4) |
-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: Nov 1, 2018 |
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: 2→46 Å / Num. obs: 125268 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6263 / CC1/2: 0.844 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.944 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.193 / 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: 35.204 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.54 Å
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Refine LS restraints |
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