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Yorodumi- PDB-5jrh: Crystal structure of Salmonella enterica acetyl-CoA synthetase (A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jrh | |||||||||
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Title | Crystal structure of Salmonella enterica acetyl-CoA synthetase (Acs) in complex with cAMP and Coenzyme A | |||||||||
Components | Acetyl-coenzyme A synthetase | |||||||||
Keywords | LIGASE / acetyl-Coenzyme A synthetase / cAMP / AMP-forming / acetyl-Coenzyme A | |||||||||
Function / homology | Function and homology information acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / acetyl-CoA biosynthetic process / AMP binding / chemotaxis / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 Å | |||||||||
Authors | Shen, L. / Zhang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Cyclic AMP Inhibits the Activity and Promotes the Acetylation of Acetyl-CoA Synthetase through Competitive Binding to the ATP/AMP Pocket. Authors: Han, X. / Shen, L. / Wang, Q. / Cen, X. / Wang, J. / Wu, M. / Li, P. / Zhao, W. / Zhang, Y. / Zhao, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jrh.cif.gz | 290.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jrh.ent.gz | 228 KB | Display | PDB format |
PDBx/mmJSON format | 5jrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jrh ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jrh | HTTPS FTP |
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-Related structure data
Related structure data | 1pg4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 73307.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: acs, STM4275 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZKF6, acetate-CoA ligase |
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-Non-polymers , 5 types, 1123 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BU3 / ( #6: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 42.1 % Description: Shell-like crystals were able to reach dimension of 0.2 mm x 0.4 mm x 0.1 mm. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 0.2 M KH2PO4, pH 4.8, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9782 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 1.644→40 Å / Num. obs: 147320 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PG4 Resolution: 1.644→37.576 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.644→37.576 Å
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Refine LS restraints |
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LS refinement shell |
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