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- PDB-4ygo: Dodecameric structure of spermidine N-acetyltransferase from Vibr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ygo | ||||||
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Title | Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae in intermediate state | ||||||
![]() | Spermidine n1-acetyltransferase | ||||||
![]() | TRANSFERASE / SpeG / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
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. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. Authors: Filippova, E.V. / Weigand, S. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 442.2 KB | Display | ![]() |
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PDB format | ![]() | 366.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.4 KB | Display | ![]() |
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Full document | ![]() | 484.1 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jlyC ![]() 5cnpC ![]() 3eg7 C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 20703.385 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MOH / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.01 M CaCl2, 0.1 M Tris HCl, 20% Methanol, 25 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 46610 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EG7 ![]() 3eg7 Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.949 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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