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- PDB-5ug4: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ug4 | ||||||
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Title | Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae | ||||||
![]() | Spermidine N(1)-acetyltransferase | ||||||
![]() | TRANSFERASE / SpeG / spermidine / spermine / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() spermidine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / polyamine catabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.4 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.5 KB | Display | ![]() |
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Full document | ![]() | 485.6 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mi4S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 20703.385 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 251 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-MRD / ( | #5: Chemical | ChemComp-EOH / | #6: Chemical | ChemComp-MOH / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 50% MPD, 20% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2011 / Details: beryllium lenses |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 36218 / % possible obs: 99.4 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 15 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1771 / % possible all: 98.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4MI4 Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.993 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.161 / 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: 39.589 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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