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Yorodumi- PDB-8try: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8try | |||||||||||||||
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Title | Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20348 | |||||||||||||||
Components | Polyketide synthase Pks13 | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / thioesterase | |||||||||||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||||||||
Authors | Krieger, I.V. / Sacchettini, J.C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Acs Infect Dis. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8try.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8try.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 8try.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/8try ftp://data.pdbj.org/pub/pdb/validation_reports/tr/8try | HTTPS FTP |
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-Related structure data
Related structure data | 8tqgC 8tqvC 8tr4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 31777.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks13, Rv3800c / Production host: Escherichia coli (E. coli) References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-QU0 / Mass: 486.627 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H34N4O4S / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.24 % |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.36 Å / Num. obs: 25227 / % possible obs: 85.8 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.098 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.097 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2532 / CC1/2: 0.396 / Rpim(I) all: 0.604 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→48.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.28 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 49.033 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→48.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 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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