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Yorodumi- PDB-7kwh: Spermidine N-acetyltransferase SpeG K23-Y30 chimera from Vibrio c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kwh | ||||||
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Title | Spermidine N-acetyltransferase SpeG K23-Y30 chimera from Vibrio cholerae and hSSAT | ||||||
Components | Spermidine N(1)-acetyltransferase | ||||||
Keywords | TRANSFERASE / SpeG Enzyme Allosteric | ||||||
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 serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Le, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Renolo, R. / Forwood, J.K. | ||||||
Citation | Journal: Front Mol Biosci / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kwh.cif.gz | 946.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kwh.ent.gz | 645.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/7kwh ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kwh | HTTPS FTP |
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-Related structure data
Related structure data | 7kwjC 7kwqC 7kwxC 7kx2C 7kx3C 4jjxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20764.463 Da / Num. of mol.: 12 / Mutation: N23K, N24E, R25L, N26A, I27R, M28Y, S29E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: speG, VC_A0947 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KL03, diamine N-acetyltransferase #2: Chemical | ChemComp-PO4 / Has ligand of interest | N | |
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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: 3.13 Å3/Da / Density % sol: 60.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH6.5, 10% PEG5000 MME, and 12% propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 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: 2.9→39.68 Å / Num. obs: 69880 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 66.24 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 2 / Num. unique obs: 4434 / CC1/2: 0.509 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JJX Resolution: 2.9→39.68 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12 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: 68.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39.68 Å
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Refine LS restraints |
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LS refinement shell |
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