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Open data
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Basic information
Entry | Database: PDB / ID: 1mn6 | ||||||
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Title | Thioesterase Domain from Picromycin Polyketide Synthase, pH 7.6 | ||||||
![]() | polyketide synthase IV | ||||||
![]() | TRANSFERASE / thioesterase / polyketide synthase / open substrate channel / alpha-beta hydrolase | ||||||
Function / homology | ![]() 10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.M. | ||||||
![]() | ![]() Title: Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases Authors: Tsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.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 | ![]() | 122.6 KB | Display | ![]() |
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PDB format | ![]() | 96.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.2 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mnaC ![]() 1mnqC ![]() 1mo2C ![]() 1kezS 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
#1: Protein | Mass: 31485.240 Da / Num. of mol.: 2 / Fragment: Thioesterase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 30% PEG 8000, 100 mM HEPES, 2 mM DTT, 100 mM magnesium chloride, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 31231 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 203580 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KEZ Resolution: 2.2→29.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 208419.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.4463 Å2 / ksol: 0.360028 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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