[English] 日本語
Yorodumi- PDB-5ug4: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ug4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae | ||||||
Components | Spermidine N(1)-acetyltransferase | ||||||
Keywords | TRANSFERASE / SpeG / spermidine / spermine / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
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: 2.15 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ug4.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ug4.ent.gz | 187.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ug4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ug4_validation.pdf.gz | 479.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ug4_full_validation.pdf.gz | 485.6 KB | Display | |
Data in XML | 5ug4_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5ug4_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/5ug4 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/5ug4 | HTTPS FTP |
-Related structure data
Related structure data | 4mi4S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 20703.385 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Gene: speG, VC_A0947 / Plasmid: MCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic / References: UniProt: Q9KL03, diamine N-acetyltransferase |
---|
-Non-polymers , 6 types, 251 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-MRD / ( | #5: Chemical | ChemComp-EOH / | #6: Chemical | ChemComp-MOH / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 50% MPD, 20% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2011 / Details: beryllium lenses |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 36218 / % possible obs: 99.4 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 15 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1771 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MI4 Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.993 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.589 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|