+Open data
-Basic information
Entry | Database: PDB / ID: 8tuk | |||||||||||||||
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Title | Alvinella ASCC1 KH and Phosphodiesterase/Ligase Domain | |||||||||||||||
Components | Activating signal cointegrator 1 complex subunit 1 | |||||||||||||||
Keywords | RNA BINDING PROTEIN / alkylation response / RNA damage / KH domain / phosphoesterase domain / RNA ligase domain | |||||||||||||||
Function / homology | IMIDAZOLE Function and homology information | |||||||||||||||
Biological species | Alvinella pompejana (invertebrata) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||||||||
Authors | Tsutakawa, S.E. / Tainer, J.A. / Arvai, A.S. / Chinnam, N.B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase. Authors: Chinnam, N.B. / Thapar, R. / Arvai, A.S. / Sarker, A.H. / Soll, J.M. / Paul, T. / Syed, A. / Rosenberg, D.J. / Hammel, M. / Bacolla, A. / Katsonis, P. / Asthana, A. / Tsai, M.S. / Ivanov, I. ...Authors: Chinnam, N.B. / Thapar, R. / Arvai, A.S. / Sarker, A.H. / Soll, J.M. / Paul, T. / Syed, A. / Rosenberg, D.J. / Hammel, M. / Bacolla, A. / Katsonis, P. / Asthana, A. / Tsai, M.S. / Ivanov, I. / Lichtarge, O. / Silverman, R.H. / Mosammaparast, N. / Tsutakawa, S.E. / Tainer, J.A. #1: Journal: Proteins / Year: 2021 Title: Target highlights in CASP14: Analysis of models by structure providers. Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / ...Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / Fidelis, K. / Grinter, R. / Gupta, G.D. / Hartmann, M.D. / Hayes, C.S. / Heidebrecht, T. / Ilari, A. / Joachimiak, A. / Kim, Y. / Linares, R. / Lovering, A.L. / Lunin, V.V. / Lupas, A.N. / Makbul, C. / Michalska, K. / Moult, J. / Mukherjee, P.K. / Nutt, W.S. / Oliver, S.L. / Perrakis, A. / Stols, L. / Tainer, J.A. / Topf, M. / Tsutakawa, S.E. / Valdivia-Delgado, M. / Schwede, T. #2: Journal: Methods Mol.Biol. / Year: 2022 Title: Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Authors: Chinnam, N.B. / Syed, A. / Burnett, K.H. / Hura, G.L. / Tainer, J.A. / Tsutakawa, S.E. #3: Journal: Methods Enzymol. / Year: 2023 Title: Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution. Authors: Chinnam, N.B. / Syed, A. / Hura, G.L. / Hammel, M. / Tainer, J.A. / Tsutakawa, S.E. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tuk.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tuk.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tuk_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 8tuk_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 8tuk_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 8tuk_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/8tuk ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tuk | HTTPS FTP |
-Related structure data
Related structure data | 8tlyC 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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Unit cell |
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-Components
#1: Protein | Mass: 36619.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alvinella pompejana (invertebrata) / Gene: 2696536 / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% MPEG 2K, 200 mM, 200 mM I/M pH 5.0. 2.5% KCl (saturated), 0.6% BME. For cryo protection, crystals for about 2 seconds in 15% MPEG 2K, 200 mM I/M pH 5.0, 2.5% KCl (saturated), 60% ...Details: 15% MPEG 2K, 200 mM, 200 mM I/M pH 5.0. 2.5% KCl (saturated), 0.6% BME. For cryo protection, crystals for about 2 seconds in 15% MPEG 2K, 200 mM I/M pH 5.0, 2.5% KCl (saturated), 60% ethylene glycol was mixed 1:2 (cryo:reservoir) Temp details: 15 deg celcius |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→3.44 Å / Num. obs: 101451 / % possible obs: 95.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.76 Å2 / CC1/2: 0.999 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.15→1.22 Å / Redundancy: 5 % / Mean I/σ(I) obs: 5 / Num. unique obs: 13759 / CC1/2: 0.83 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→3.44 Å / SU ML: 0.0928 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 18.7934 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→3.44 Å
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Refine LS restraints |
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LS refinement shell |
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