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- PDB-5xpg: Crystal structure of T. thermophilus Argonaute protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 5xpg
TitleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand
Components
  • 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*A P*GP*T)-3'
  • 5'-R(*UP*AP*U*AP*CP*AP*AP*CP*CP*UP*AP*CP*AP*UP*AP*CP*CP*UP*CP* G)-3'
  • Uncharacterized protein
KeywordsDNA BINDING PROTEIN / Argonaute / miRNA / bulge / mismatch
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding
Similarity search - Function
Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, J.D. / Wang, Y.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.
Authors: Sheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D.J. / Wang, Y.
History
DepositionJun 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
C: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*A P*GP*T)-3'
G: 5'-R(*UP*AP*U*AP*CP*AP*AP*CP*CP*UP*AP*CP*AP*UP*AP*CP*CP*UP*CP* G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8046
Polymers89,5883
Non-polymers2163
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-81 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.351, 202.351, 202.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Protein / DNA chain / RNA chain , 3 types, 3 molecules ACG

#1: Protein Uncharacterized protein / Argonaute


Mass: 76727.750 Da / Num. of mol.: 1 / Mutation: D546N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0026 / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)plyss / References: UniProt: Q746M7
#2: DNA chain 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*A P*GP*T)-3'


Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#3: RNA chain 5'-R(*UP*AP*U*AP*CP*AP*AP*CP*CP*UP*AP*CP*AP*UP*AP*CP*CP*UP*CP* G)-3'


Mass: 6271.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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Non-polymers , 3 types, 26 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 M (NH4)2SO4, 0.1 M KCL, 10 MM MGCL2, 50 MM BIS-TRIS PH 6.5 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 308K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35223 / % possible obs: 99.5 % / Redundancy: 8.7 % / Biso Wilson estimate: 53.86 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIXPHENIX.REFINErefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DLH

3dlh


Resolution: 2.8→49.08 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.16
RfactorNum. reflection% reflection
Rfree0.246 1761 5.01 %
Rwork0.203 --
obs0.205 35178 99.5 %
Solvent computationBsol: 43.9 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 57.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 774 11 23 6044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076236
X-RAY DIFFRACTIONf_angle_d1.2018654
X-RAY DIFFRACTIONf_dihedral_angle_d19.8492374
X-RAY DIFFRACTIONf_chiral_restr0.069968
X-RAY DIFFRACTIONf_plane_restr0.005998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.802-2.8770.3681390.3232482X-RAY DIFFRACTION98
2.877-2.9620.3491320.2892492X-RAY DIFFRACTION100
2.962-3.0570.3261370.2682533X-RAY DIFFRACTION100
3.057-3.1670.281170.2332556X-RAY DIFFRACTION100
3.167-3.2930.2811340.2192511X-RAY DIFFRACTION100
3.293-3.4430.2941430.2162544X-RAY DIFFRACTION100
3.443-3.6250.2661210.1972561X-RAY DIFFRACTION100
3.625-3.8520.2281200.182570X-RAY DIFFRACTION100
3.852-4.1490.2131460.1712561X-RAY DIFFRACTION100
4.149-4.5670.1791310.162596X-RAY DIFFRACTION100
4.567-5.2270.1951550.1532582X-RAY DIFFRACTION100
5.227-6.5820.2051390.1872642X-RAY DIFFRACTION100
6.582-49.0850.2361470.2022787X-RAY DIFFRACTION99

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