+Open data
-Basic information
Entry | Database: PDB / ID: 1pg3 | |||||||||
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Title | Acetyl CoA Synthetase, Acetylated on Lys609 | |||||||||
Components | acetyl-CoA synthetase | |||||||||
Keywords | LIGASE / AMP-forming / Adenylate-forming / thioester-forming / Lysine acetylation | |||||||||
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 enterica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | |||||||||
Authors | Gulick, A.M. / Starai, V.J. / Horswill, A.R. / Homick, K.M. / Escalante-Semerena, J.C. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 Title: The 1.75 A Crystal Structure of Acetyl-CoA Synthetase Bound to Adenosine-5'-propylphosphate and Coenzyme A Authors: Gulick, A.M. / Starai, V.J. / Horswill, A.R. / Homick, K.M. / 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 | 1pg3.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pg3.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 1pg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pg3 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pg3 | HTTPS FTP |
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-Related structure data
Related structure data | 1pg4C 1nnm C: citing same article (ref.) 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: 72182.422 Da / Num. of mol.: 2 / Mutation: R174C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: ACS / Plasmid: pTYB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZKF6, acetate-CoA ligase |
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-Non-polymers , 5 types, 389 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #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: 41.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 2002 / Details: Osmic Max-Flux confocal focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→24.21 Å / Num. all: 53761 / Num. obs: 51511 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.29→2.38 Å / Mean I/σ(I) obs: 1.7 / Num. unique all: 4037 / Rsym value: 0.384 / % possible all: 78.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 177381 / % possible obs: 95.9 % / Num. measured all: 51552 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 78.3 % / Num. unique obs: 4037 / Num. measured obs: 9516 / Rmerge(I) obs: 0.384 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1NNM 1nnm Resolution: 2.3→24.22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.06 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→24.22 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.199 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.25 |