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- PDB-8tuk: Alvinella ASCC1 KH and Phosphodiesterase/Ligase Domain -

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Basic information

Entry
Database: PDB / ID: 8tuk
TitleAlvinella ASCC1 KH and Phosphodiesterase/Ligase Domain
ComponentsActivating signal cointegrator 1 complex subunit 1
KeywordsRNA BINDING PROTEIN / alkylation response / RNA damage / KH domain / phosphoesterase domain / RNA ligase domain
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsTsutakawa, S.E. / Tainer, J.A. / Arvai, A.S. / Chinnam, N.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP180813 United States
Robert A. Welch FoundationRP180813 United States
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
DepositionAug 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activating signal cointegrator 1 complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0688
Polymers36,6191
Non-polymers4497
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.880, 51.599, 81.927
Angle α, β, γ (deg.)90.000, 91.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Activating signal cointegrator 1 complex subunit 1


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)
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1692 1929 1.95 %
Rwork0.1461 97025 -
obs0.1466 98954 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.48 Å2
Refinement stepCycle: LAST / Resolution: 1.15→3.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 30 431 2801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772559
X-RAY DIFFRACTIONf_angle_d0.87053466
X-RAY DIFFRACTIONf_chiral_restr0.0789372
X-RAY DIFFRACTIONf_plane_restr0.0073465
X-RAY DIFFRACTIONf_dihedral_angle_d12.23481012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.2894950.25754791X-RAY DIFFRACTION65.21
1.18-1.210.2371210.23075907X-RAY DIFFRACTION79.63
1.21-1.250.2221280.2026842X-RAY DIFFRACTION92.8
1.25-1.290.22111400.18076997X-RAY DIFFRACTION94.34
1.29-1.330.20311430.17117005X-RAY DIFFRACTION94.81
1.33-1.390.18631390.16187108X-RAY DIFFRACTION95.92
1.39-1.450.17551480.14547180X-RAY DIFFRACTION97.51
1.45-1.530.15311420.13177210X-RAY DIFFRACTION97.27
1.53-1.620.13981440.12967219X-RAY DIFFRACTION97.06
1.62-1.750.17561430.1367284X-RAY DIFFRACTION98.41
1.75-1.920.16081430.13377307X-RAY DIFFRACTION98
1.92-2.20.14561500.12827310X-RAY DIFFRACTION98.49
2.2-2.770.17451410.14397369X-RAY DIFFRACTION98.18
2.77-3.440.16741520.14837496X-RAY DIFFRACTION98.86

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