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Yorodumi- PDB-4r87: Crystal structure of spermidine N-acetyltransferase from Vibrio c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r87 | ||||||
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Title | Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with CoA and spermine | ||||||
Components | Spermidine n1-acetyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / coenzyme A / spermidine / spermine | ||||||
Function / homology | Function and homology information 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 | Vibrio cholerae O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure. Authors: Filippova, E.V. / Kuhn, M.L. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Ballicora, M.A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r87.cif.gz | 850.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r87.ent.gz | 718.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r87_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 4r87_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 4r87_validation.xml.gz | 90.5 KB | Display | |
Data in CIF | 4r87_validation.cif.gz | 112.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r87 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r87 | HTTPS FTP |
-Related structure data
Related structure data | 4jjxC 4mhdC 4mi4C 4nczC 4r57C 3eg7 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20975.646 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q9KL03 #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-SPM / #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: Nov 26, 2013 / Details: Beryllium lenses | |||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→50 Å / Num. all: 68437 / Num. obs: 68437 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 15.04 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EG7 3eg7 Resolution: 2.61→43.82 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.018 / SU ML: 0.187 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.072 / 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: 37.435 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→43.82 Å
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Refine LS restraints |
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