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Open data
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Basic information
Entry | Database: PDB / ID: 5tv8 | ||||||
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Title | A. aeolicus BioW with AMP-CPP and pimelate | ||||||
![]() | 6-carboxyhexanoate--CoA ligase | ||||||
![]() | LIGASE / Pimeloyl-CoA Ligase / adenylation | ||||||
Function / homology | ![]() 6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / biotin biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Estrada, P. / Manandhar, M. / Dong, S.-H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K. | ||||||
![]() | ![]() Title: The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. Authors: Estrada, P. / Manandhar, M. / Dong, S.H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 87.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27445.881 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / Details: 20-30% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 29, 2016 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→48 Å / Num. obs: 27824 / % possible obs: 99.5 % / Redundancy: 8 % / Rsym value: 0.103 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.55→2.56 Å / Num. unique all: 1936 / Rsym value: 0.938 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.266 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→25 Å
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Refine LS restraints |
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