+Open data
-Basic information
Entry | Database: PDB / ID: 4nxy | ||||||
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Title | Crystal Structure of the GNAT domain of S. lividans PAT | ||||||
Components | Acyl-CoA synthetaseAcetyl-CoA synthetase | ||||||
Keywords | TRANSFERASE / Lysine Acetyltransferase / AMP-Forming Acetate:CoA Ligase Enzyme (Acs) | ||||||
Function / homology | Function and homology information N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.449 Å | ||||||
Authors | Rank, K.C. / Tucker, A.C. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Insights into the specificity of lysine acetyltransferases. Authors: Tucker, A.C. / Taylor, K.C. / Rank, K.C. / Rayment, I. / Escalante-Semerena, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nxy.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nxy.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxy ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxy | HTTPS FTP |
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-Related 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: 21653.266 Da / Num. of mol.: 1 / Fragment: GNAT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: TK24 / Gene: SSPG_01886 / Production host: Escherichia coli (E. coli) / References: UniProt: D6EP29, UniProt: A0A7U8YS53*PLUS |
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#2: Chemical | ChemComp-ETF / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.62 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: 22% monomethyl polyethylene glycol 5000, 100 mM MOPS pH 7.0, 25 mM MgCl2, 2% 2,2,2-trifluoroethanol, 6% glycerol, Batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97936 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2012 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→25 Å / Num. all: 30626 / Num. obs: 30540 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 58.854 |
Reflection shell | Resolution: 1.449→1.48 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 10.07 / Num. unique all: 1475 / Rsym value: 0.212 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.449→24.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.208 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.075 / 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: 15.384 Å2
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Refinement step | Cycle: LAST / Resolution: 1.449→24.52 Å
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Refine LS restraints |
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