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Open data
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Basic information
Entry | Database: PDB / ID: 8ahz | ||||||||||||
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Title | Native VirD of Streptomyces virginiae | ||||||||||||
![]() | Enoyl-CoA hydratase | ||||||||||||
![]() | BIOSYNTHETIC PROTEIN / Enoyl-CoA hydratase / Beta-methylation / Antibiotic / ACP / Polyketide / PKS | ||||||||||||
Function / homology | Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / catalytic activity / IMIDAZOLE / Enoyl-CoA hydratase![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Collin, S. / Gruez, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Decrypting the programming of beta-methylation in virginiamycin M biosynthesis. Authors: Collin, S. / Cox, R.J. / Paris, C. / Jacob, C. / Chagot, B. / Weissman, K.J. / Gruez, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.8 KB | Display | ![]() |
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PDB format | ![]() | 224.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a7zC ![]() 8ahqC ![]() 8aigC ![]() 8allC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 26356.830 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IMD / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 400, 20% PEG 800, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953709 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.7→59.62 Å / Num. obs: 87602 / % possible obs: 99 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.021 / Rrim(I) all: 0.074 / Net I/σ(I): 19.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 80.26 Å2 / Biso mean: 27.189 Å2 / Biso min: 17.09 Å2
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Refinement step | Cycle: final / Resolution: 1.7→57.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / 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 |
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