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Yorodumi- PDB-4ncz: Spermidine N-acetyltransferase from Vibrio cholerae in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ncz | |||||||||
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Title | Spermidine N-acetyltransferase from Vibrio cholerae in complex with 2-[n-cyclohexylamino]ethane sulfonate. | |||||||||
Components | Spermidine n1-acetyltransferase | |||||||||
Keywords | TRANSFERASE / Structural genomics / spermidine N1-acetyltransferase / IDP01616 / 2-[n-cyclohexylamino]ethane sulfonate / CHES / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information polyamine catabolic process / spermidine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Osipiuk, J. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / 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 | 4ncz.cif.gz | 236.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ncz.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ncz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/4ncz ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4ncz | HTTPS FTP |
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-Related structure data
Related structure data | 4jjxC 4mhdC 4mi4C 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 21116.330 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KL03 |
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-Non-polymers , 5 types, 288 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: 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: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.2 M lithium sulfate, 0.1 M CHES buffer, 1 M potassium/sodium tartrate, 0.02 M acetylcholine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 16, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→32.02 Å / Num. all: 52181 / Num. obs: 52181 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EG7 3eg7 Resolution: 1.89→32.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 7.153 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.143 / 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: 43.139 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→32.02 Å
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Refine LS restraints |
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