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Yorodumi- PDB-7kvy: Crystal Structure of Acetyl-CoA synthetase in complex with adenos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kvy | ||||||
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Title | Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate and Co-enzyme A from Coccidioides immitis RS | ||||||
Components | Acetyl-coenzyme A synthetase | ||||||
Keywords | LIGASE / SSGCID / Acetyl-coenzyme A synthetase / ethyl-AMP / CoA / Co-Enzyme A / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding Similarity search - Function | ||||||
Biological species | Coccidioides immitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate and Co-enzyme A from Coccidioides immitis RS Authors: Fox III, D. / Abendroth, J. / DeBouver, N.D. / Esan, T.E. / Hagen, T.J. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kvy.cif.gz | 274.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kvy.ent.gz | 218.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kvy ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kvy | HTTPS FTP |
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-Related structure data
Related structure data | 7kcpS 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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Unit cell |
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-Components
#1: Protein | Mass: 78435.828 Da / Num. of mol.: 1 / Fragment: CoimA.00629.a.FS11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus) Strain: RS / Gene: CIMG_01510 / Plasmid: CoimA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3KJC6, acetate-CoA ligase | ||||
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#2: Chemical | ChemComp-COA / | ||||
#3: Chemical | ChemComp-WTA / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Optimization conditions around RigakuReagents JCSG H3: 18.32@ PEG3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'- ...Details: Optimization conditions around RigakuReagents JCSG H3: 18.32@ PEG3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'-ethylphosphate + 1mM Co-EnzymeA; Cryo: 20% ethylene glycol; tray 317944f5, puck dzd7-5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 24, 2020 / Details: Beryllium Lenses |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 59143 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 33.21 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.29 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.09 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KCP Resolution: 1.9→46.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.35 / 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: 47.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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