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Yorodumi- PDB-4u5y: Crystal Structure of the complex between the GNAT domain of S. li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u5y | |||||||||
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Title | Crystal Structure of the complex between the GNAT domain of S. lividans PAT and the acetyl-CoA synthetase C-terminal domain of S. enterica | |||||||||
Components |
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Keywords | LIGASE / GNAT / COMPLEX / ACETYLATION / PAT | |||||||||
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 TK24 (bacteria) Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.926 Å | |||||||||
Authors | Taylor, K.C. / Tucker, A.C. / Rank, K.C. / Escalante-Semerena, J.C. / Rayment, I. | |||||||||
Funding support | United States, 2items
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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 | 4u5y.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u5y.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 4u5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/4u5y ftp://data.pdbj.org/pub/pdb/validation_reports/u5/4u5y | HTTPS FTP |
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-Related structure data
Related structure data | 4nxySC 1pg4S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21669.332 Da / Num. of mol.: 1 / Fragment: UNP residues 1-194 / Mutation: S73C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans TK24 (bacteria) / Gene: SSPG_01886 / Production host: Escherichia coli (E. coli) / References: UniProt: D6EP29, UniProt: A0A7U8YS53*PLUS | ||
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#2: Protein | Mass: 14535.637 Da / Num. of mol.: 1 / Fragment: UNP residues 518-652 / Mutation: H567C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719 (bacteria) Gene: acs, SEEPB719_19728 / Production host: Escherichia coli (E. coli) / References: UniProt: V1Q8H8, acetate-CoA ligase | ||
#3: Chemical | #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: 1.99 Å3/Da / Density % sol: 38.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 11.2% (w/v) polyethylene glycol 8000, 100 mM 1,4-piperazinediethanesulfonic acid pH 6.5, 120 mM Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 14, 2014 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 22055 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.067 / Net I/av σ(I): 30.5 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / % possible all: 98.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NXY, 1PG4 Resolution: 1.926→21.632 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.63 / Stereochemistry target values: ML
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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: 18.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.926→21.632 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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