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- PDB-4yaj: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yaj | ||||||
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Title | Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 (apo form) | ||||||
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![]() | LIGASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD | ||||||
Function / homology | ![]() acetate-CoA ligase (ADP-forming) activity / nucleotide binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Weisse, R.H.-J. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Authors: Weie, R.H. / Faust, A. / Schmidt, M. / Schonheit, P. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 481.6 KB | Display | ![]() |
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PDB format | ![]() | 400.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 62.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xylC ![]() 4xymC ![]() 4xz3C ![]() 4y8vC ![]() 4yakC ![]() 4yb8C ![]() 4ybzC ![]() 5hbrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49354.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 25676.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % / Description: rod-like appearance |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris/HCl pH 8.5, 14% (w/v) PEG6000, 6.3 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→125.81 Å / Num. all: 73935 / Num. obs: 73935 / % possible obs: 97.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.239 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.1 % / Rmerge(I) obs: 2.162 / Mean I/σ(I) obs: 0.4 / % possible all: 57 |
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Processing
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Refinement | Resolution: 2.2→83.337 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.55 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→83.337 Å
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Refine LS restraints |
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LS refinement shell |
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