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- PDB-8tqv: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tqv | |||||||||||||||
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Title | Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20403 | |||||||||||||||
![]() | Polyketide synthase Pks13 | |||||||||||||||
![]() | BIOSYNTHETIC PROTEIN / polyketide synthase / thioesterase | |||||||||||||||
Function / homology | ![]() DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Krieger, I.V. / Sacchettini, J.C. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / ...Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / Gengenbacher, M. / Guie, M.A. / Guilinger, J.P. / Bienstock, C. / Hartl, H. / Hupp, C.D. / Jetson, R. / Satoh, T. / Yeoman, J.T.S. / Zhang, Y. / Dartois, V. / Schnappinger, D. / Keefe, A.D. / Sacchettini, J.C. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.9 KB | Display | ![]() |
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PDB format | ![]() | 184.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 945.8 KB | Display | ![]() |
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Full document | ![]() | 949.5 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tqgC ![]() 8tr4C ![]() 8tryC 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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Unit cell |
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Components
#1: Protein | Mass: 30646.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: pks13 / Production host: ![]() ![]() References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | Mass: 541.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H35N5O4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-SO4 / #4: 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: 2.84 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM SULFATE, 2%-5% V/V PPG P400 |
-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: Sep 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.49 Å / Num. obs: 46267 / % possible obs: 98.9 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3415 / CC1/2: 0.644 / Rpim(I) all: 0.569 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.194 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / 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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