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- PDB-7kwj: Spermidine N-acetyltransferase SpeG K23-Q34 chimera from Vibrio c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kwj | ||||||
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Title | Spermidine N-acetyltransferase SpeG K23-Q34 chimera from Vibrio cholerae and hSSAT | ||||||
![]() | Spermidine N(1)-acetyltransferase | ||||||
![]() | TRANSFERASE / SpeG Enzyme Allosteric | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Le, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Renolo, R. / Forwood, J.K. / Kuhn, M.L. | ||||||
![]() | ![]() Title: The Vibrio cholerae SpeG Spermidine/Spermine N -Acetyltransferase Allosteric Loop and beta 6-beta 7 Structural Elements Are Critical for Kinetic Activity. Authors: Le, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Lim, E.Q. / Renolo, R. / Forwood, J.K. / Kuhn, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.9 KB | Display | ![]() |
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PDB format | ![]() | 158.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 450.7 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kwhC ![]() 7kwqC ![]() 7kwxC ![]() 7kx2C ![]() 7kx3C ![]() 4jjxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20690.404 Da / Num. of mol.: 3 Mutation: N23K, N24E, R25L, N26A, I27R, M28Y, S29E, W31M, F32E, E34Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: speG, VC_A0947 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 2M sodium formate, 0.1M sodium acetate pH5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→29.97 Å / Num. obs: 1878 / % possible obs: 98.3 % / Redundancy: 4 % / Biso Wilson estimate: 54.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.58→2.676 Å / Num. unique obs: 202 / CC1/2: 0.919 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JJX Resolution: 2.58→29.97 Å / SU ML: 0.3747 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9069 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→29.97 Å
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Refine LS restraints |
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LS refinement shell |
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