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- PDB-6qmm: Crystal structure of Synecochoccus Spermidine Synthase in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qmm | ||||||
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Title | Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA | ||||||
![]() | (Polyamine aminopropyltransferase) x 2 | ||||||
![]() | TRANSFERASE / Synthase / Homodimer | ||||||
Function / homology | ![]() spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guedez, G. / Pothipongsa, A. / Incharoensakdi, A. / Salminen, T.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of dimericSynechococcusspermidine synthase with bound polyamine substrate and product. Authors: Guedez, G. / Pothipongsa, A. / Siren, S. / Liljeblad, A. / Jantaro, S. / Incharoensakdi, A. / Salminen, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.8 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yuvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31451.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7942 / Gene: speE, Synpcc7942_0628 / Plasmid: pET22b / Production host: ![]() ![]() |
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#2: Protein | Mass: 31346.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7942 / Gene: speE, Synpcc7942_0628 / Plasmid: pET22b / Production host: ![]() ![]() |
-Non-polymers , 5 types, 260 molecules ![](data/chem/img/PUT.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/PXN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/PXN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PUT / |
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#4: Chemical | ChemComp-SPD / |
#5: Chemical | ChemComp-MTA / |
#6: Chemical | ChemComp-PXN / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.0, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→48.17 Å / Num. obs: 27391 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0721 / Rrim(I) all: 0.083 / Net I/σ(I): 16.18 |
Reflection shell | Resolution: 2.18→2.27 Å / Rmerge(I) obs: 0.226 / CC1/2: 0.956 / Rrim(I) all: 0.261 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YUV Resolution: 2.18→48.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.181 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 83.54 Å2 / Biso mean: 17.36 Å2 / Biso min: 6.31 Å2
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Refinement step | Cycle: final / Resolution: 2.18→48.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.181→2.238 Å / Total num. of bins used: 20
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