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Yorodumi- PDB-3uwo: Structure Guided Development of Novel Thymidine Mimetics targetin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uwo | ||||||
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Title | Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa Thymidylate Kinase: from Hit to Lead Generation | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Thymidylate kinase / kinase / thymidine triphosphate / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Choi, J.Y. / Plummer, M.S. / Starr, J. / Desbonnet, C.R. / Soutter, H.H. / Chang, J. / Miller, J.R. / Dillman, K. / Miller, A.A. / Roush, W.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation. Authors: Choi, J.Y. / Plummer, M.S. / Starr, J. / Desbonnet, C.R. / Soutter, H. / Chang, J. / Miller, J.R. / Dillman, K. / Miller, A.A. / Roush, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uwo.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uwo.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 3uwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uwo_validation.pdf.gz | 985.8 KB | Display | wwPDB validaton report |
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Full document | 3uwo_full_validation.pdf.gz | 995 KB | Display | |
Data in XML | 3uwo_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3uwo_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/3uwo ftp://data.pdbj.org/pub/pdb/validation_reports/uw/3uwo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24086.398 Da / Num. of mol.: 2 / Fragment: Kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2962, tmk / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9HZN8, dTMP kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: The protein was mixed 1:1 with a reservoir solution containing 30% PEG 4000, 0.2M MgCl2, and 0.1 M Tris pH 7.5 - 8.5 and incubated at 22C. , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→32.1 Å / Num. all: 43285 / Num. obs: 155047 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 28.65 Å2 / Rsym value: 0.051 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1419 / Rsym value: 0.247 / % possible all: 61.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.08 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Total num. of bins used: 9
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