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- PDB-5xq2: Crystal structure of T. thermophilus Argonaute protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 5xq2
TitleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand
Components
  • DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(*AP*GP*T)-3')
  • DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • TtAgo (D546N)
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) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsSheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D. / Wang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Natural Science Foundation of China31571335 China
Natural Science Foundation of China31630015 China
Natural Science Foundation of China91440201 China
Chinese Ministry of Science and Technology2014CB910102 China
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 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TtAgo (D546N)
X: DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
Y: DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
C: DNA (5'-D(*AP*GP*T)-3')
B: TtAgo (D546N)
E: DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
F: DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
D: DNA (5'-D(*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,52810
Polymers180,4798
Non-polymers492
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-103 kcal/mol
Surface area62210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.843, 201.843, 201.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TtAgo (D546N) / Uncharacterized protein


Mass: 76727.750 Da / Num. of mol.: 2 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q746M7

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DNA chain , 3 types, 6 molecules XEYFCD

#2: DNA chain DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')


Mass: 6901.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#3: DNA chain DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')


Mass: 5708.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#4: DNA chain DNA (5'-D(*AP*GP*T)-3')


Mass: 901.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop
Details: 2.8 M Na-acetate, pH7.0, 0.1M Tris-Cl, pH 8.0 and 0.15 M glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. obs: 40665 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 45.5
Reflection shellResolution: 3.32→3.38 Å / Redundancy: 26.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPY

4kpy


Resolution: 3.33→48.95 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 1846 4.95 %
Rwork0.252 --
obs0.254 37315 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10369 1470 2 3 11844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312268
X-RAY DIFFRACTIONf_angle_d1.70316996
X-RAY DIFFRACTIONf_dihedral_angle_d24.6894590
X-RAY DIFFRACTIONf_chiral_restr0.1441881
X-RAY DIFFRACTIONf_plane_restr0.0091968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3246-3.41440.2925180.2578366X-RAY DIFFRACTION13
3.4144-3.51490.36481270.29422501X-RAY DIFFRACTION85
3.5149-3.62830.32951400.2782923X-RAY DIFFRACTION100
3.6283-3.75790.30541560.28722968X-RAY DIFFRACTION100
3.7579-3.90830.34351450.26932907X-RAY DIFFRACTION100
3.9083-4.08610.28831420.27072974X-RAY DIFFRACTION100
4.0861-4.30140.2751560.25262926X-RAY DIFFRACTION100
4.3014-4.57080.30581570.24942926X-RAY DIFFRACTION100
4.5708-4.92340.32171800.23692979X-RAY DIFFRACTION100
4.9234-5.41820.30481650.2442918X-RAY DIFFRACTION100
5.4182-6.20090.31381390.26343009X-RAY DIFFRACTION100
6.2009-7.80740.32411310.23463021X-RAY DIFFRACTION100
7.8074-48.95940.20271900.20593051X-RAY DIFFRACTION99

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