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Yorodumi- PDB-4mhd: Crystal structure of spermidine N-acetyltransferase from Vibrio c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mhd | ||||||
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Title | Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermidine | ||||||
Components | Spermidine n1-acetyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine / N-acetyltransferase | ||||||
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 biovar El Tor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / 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 | 4mhd.cif.gz | 235.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhd.ent.gz | 192.4 KB | Display | PDB format |
PDBx/mmJSON format | 4mhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mhd_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 4mhd_full_validation.pdf.gz | 470.2 KB | Display | |
Data in XML | 4mhd_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4mhd_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhd ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhd | HTTPS FTP |
-Related structure data
Related structure data | 4jjxC 4mi4C 4nczC 4r57C 4r87C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23447.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (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 | #3: 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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M NaCl, 30% Ethanol, 0.1M Tris HCl, pH 8.5, 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 12, 2011 / 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 | Resolution: 2.3→30 Å / Num. all: 30239 / Num. obs: 30239 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 7.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EG7 3eg7 Resolution: 2.32→29.33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.659 / SU ML: 0.169 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.239 / 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: 54.973 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→29.33 Å
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Refine LS restraints |
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