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- PDB-5mg5: A multi-component acyltransferase PhlABC from Pseudomonas protege... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mg5 | ||||||
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Title | A multi-component acyltransferase PhlABC from Pseudomonas protegens soaked with the monoacetylphloroglucinol (MAPG) | ||||||
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![]() | TRANSFERASE / acyltransferase / Pseudomonas protegens / PhlABC / multi-component / MAPG | ||||||
Function / homology | Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase-like / benzene-1,3,5-triol / : / : / 2,4-diacetylphloroglucinol biosynthesis protein PhlC![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pavkov-Keller, T. / Schmidt, N.G. / Kroutil, W. / Gruber, K. | ||||||
![]() | ![]() Title: Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase. Authors: Pavkov-Keller, T. / Schmidt, N.G. / Zadlo-Dobrowolska, A. / Kroutil, W. / Gruber, 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 | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.3 KB | Display | ![]() |
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Full document | ![]() | 714.9 KB | Display | |
Data in XML | ![]() | 232.4 KB | Display | |
Data in CIF | ![]() | 314.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m3kSC S: Starting model for refinement 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
-Protein , 1 types, 8 molecules ADGJMPSV
#1: Protein | Mass: 38565.480 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-2,4-diacetylphloroglucinol biosynthesis ... , 2 types, 16 molecules BEHKNQTWCFILORUX
#2: Protein | Mass: 16666.434 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 42581.941 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: phlC, PFL_5955 / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 74 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/13X.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/13X.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-13X / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: Index screen #55 (0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 0% v/v Polyethylene glycol monomethyl ether 550). 12mg/ml in potassium phosphate buffer, 50 mM, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3.44→49.72 Å / Num. obs: 99724 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.268 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.44→3.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.57 / CC1/2: 0.81 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M3K Resolution: 3.44→49.725 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.47 / 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: 3.44→49.725 Å
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Refine LS restraints |
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LS refinement shell |
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