+Open data
-Basic information
Entry | Database: PDB / ID: 2p2b | ||||||
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Title | Acetyl-CoA Synthetase, V386A mutation | ||||||
Components | Acetyl-coenzyme A synthetase | ||||||
Keywords | LIGASE / Adenylate-forming enzymes / Domain Alternation / Acyl-CoA ligase | ||||||
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: 2.2 Å | ||||||
Authors | Reger, A.S. / Gulick, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Biochemical and Crystallographic Analysis of Substrate Binding and Conformational Changes in Acetyl-CoA Synthetase. Authors: Reger, A.S. / Carney, J.M. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p2b.cif.gz | 261.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p2b.ent.gz | 208.8 KB | Display | PDB format |
PDBx/mmJSON format | 2p2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/2p2b ftp://data.pdbj.org/pub/pdb/validation_reports/p2/2p2b | HTTPS FTP |
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-Related structure data
Related structure data | 2p20C 2p2fC 2p2jC 2p2mC 2p2qC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72208.422 Da / Num. of mol.: 2 / Mutation: V386A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: Typhi / 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 #2: Chemical | #3: Chemical | #4: 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: 41.9 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Propyl-AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 28, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 59117 / % possible obs: 96.9 % / Rmerge(I) obs: 0.047 / Χ2: 0.574 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.148 / Num. unique all: 5617 / Χ2: 0.346 / % possible all: 92.6 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PG4 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.442 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.205 / 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: 24.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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