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Yorodumi- 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 | ||||||
Components | Spermidine n1-acetyltransferase | ||||||
Keywords | TRANSFERASE / SpeG / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
| Function / homology | Function and homology informationpolyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
| Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
| Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2015Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4ygo.cif.gz | 442.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4ygo.ent.gz | 366.9 KB | Display | PDB format |
| PDBx/mmJSON format | 4ygo.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4ygo_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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| Full document | 4ygo_full_validation.pdf.gz | 484.1 KB | Display | |
| Data in XML | 4ygo_validation.xml.gz | 37.1 KB | Display | |
| Data in CIF | 4ygo_validation.cif.gz | 51.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4ygo ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4ygo | 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 | |
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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.) Vibrio cholerae serotype O1 (ATCC 39315 / El Tor Inaba N16961) (bacteria)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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
| 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: MOLECULAR REPLACEMENTStarting 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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About Yorodumi



Vibrio cholerae serotype O1 (bacteria)
X-RAY DIFFRACTION
United States, 1items
Citation



















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