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- PDB-4iqw: Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iqw | ||||||
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Title | Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA | ||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR/DNA / terminal transferase / TRANSFERASE-TRANSFERASE INHIBITOR-DNA complex | ||||||
Function / homology | ![]() DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gouge, J. / Delarue, M. | ||||||
![]() | ![]() Title: New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target. Authors: Costi, R. / Cuzzucoli Crucitti, G. / Pescatori, L. / Messore, A. / Scipione, L. / Tortorella, S. / Amoroso, A. / Crespan, E. / Campiglia, P. / Maresca, B. / Porta, A. / Granata, I. / ...Authors: Costi, R. / Cuzzucoli Crucitti, G. / Pescatori, L. / Messore, A. / Scipione, L. / Tortorella, S. / Amoroso, A. / Crespan, E. / Campiglia, P. / Maresca, B. / Porta, A. / Granata, I. / Novellino, E. / Gouge, J. / Delarue, M. / Maga, G. / Di Santo, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 127 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 703.5 KB | Display | ![]() |
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Full document | ![]() | 706.7 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iqtC ![]() 4iquC ![]() 4iqvC ![]() 1jmsS C: citing same article ( S: Starting model for refinement |
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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: 43628.734 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: L398A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-1FQ / ( |
#5: Water | ChemComp-HOH / |
Sequence details | PROTEIN FRAGMENT IS THE CATALYTIC CORE OF THE TDT-S (TDT-SMALL) ISOFORM (UNP RESIDUES 132-482, 503-530). |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG4000, 200 mM sodium formate, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2012 / Details: Kirkpatrick-Baez pair of bi-morph mirrors |
Radiation | Monochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.5 Å / Num. all: 14577 / Num. obs: 14429 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 59.25 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2089 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JMS Resolution: 2.6→47.49 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9011 / SU R Cruickshank DPI: 0.594 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.858 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.275 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.81 Å / Total num. of bins used: 7
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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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