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Open data
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Basic information
Entry | Database: PDB / ID: 8qd3 | ||||||
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Title | Ayg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene | ||||||
![]() | Pigment biosynthesis protein yellowish-green 1 | ||||||
![]() | LYASE / Natural Product Biosynthesis / Polyketide Synthase System / alpha / beta-Hydrolase Fold / Polyketide Shortening / Retro Claisen Reaction | ||||||
Function / homology | Esterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold / FLAVIOLIN / TRIETHYLENE GLYCOL / : / Heptaketide hydrolyase ayg1![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments. Authors: Schmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 663.4 KB | Display | ![]() |
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PDB format | ![]() | 551.9 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 | ![]() | 65 KB | Display | |
Data in CIF | ![]() | 93.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qbhC ![]() 8qbiC ![]() 8qd1C ![]() 8qd2C ![]() 8qd4C ![]() 8qd5C ![]() 8qd6C ![]() 8qd7C ![]() 8qd8C ![]() 8qd9C ![]() 8qdaC ![]() 8qdbC 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 47440.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1043 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/FLV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FLV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-QW8 / Mass: 192.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-FLV / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM K/Na tartrate, 25.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 173708 / % possible obs: 94.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 27645 / % possible all: 95.7 |
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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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.791 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→46.48 Å
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Refine LS restraints |
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