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- PDB-5xp8: Crystal structure of T. thermophilus Argonaute protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 5xp8
TitleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand
Components
  • DNA (5'-D(*AP*GP*T)-3')
  • DNA (5'-D(*CP*AP*AP*CP*C*AP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*TP*GP*AP*GP*AP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • TtAgo
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
paz domain - #50 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain / Piwi domain profile. / Piwi domain ...paz domain - #50 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, J.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
the 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 1, 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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,3137
Polymers90,2414
Non-polymers733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-74 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.140, 202.140, 202.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein TtAgo / Uncharacterized protein


Mass: 76728.734 Da / Num. of mol.: 1
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
#2: DNA chain DNA (5'-D(P*TP*GP*AP*GP*AP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')


Mass: 6901.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#3: DNA chain DNA (5'-D(*CP*AP*AP*CP*C*AP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')


Mass: 5708.726 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop
Details: 2.6 M Na-acetate, pH 7.0, 0.1M Tris-Cl, pH 7.4 and 0.2 M glycine

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: AREA DETECTOR / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25862 / % possible obs: 98.9 % / Redundancy: 6.6 % / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPY

4kpy


Resolution: 3.1→45.2 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.86
RfactorNum. reflection% reflection
Rfree0.276 1313 5.08 %
Rwork0.214 --
obs0.217 25862 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5091 714 3 0 5808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226033
X-RAY DIFFRACTIONf_angle_d1.6338350
X-RAY DIFFRACTIONf_dihedral_angle_d17.7072210
X-RAY DIFFRACTIONf_chiral_restr0.064939
X-RAY DIFFRACTIONf_plane_restr0.009966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1014-3.22560.36091380.31972667X-RAY DIFFRACTION99
3.2256-3.37230.33271780.31612647X-RAY DIFFRACTION99
3.3723-3.550.37841220.31512683X-RAY DIFFRACTION99
3.55-3.77240.35631260.29562705X-RAY DIFFRACTION99
3.7724-4.06350.33511410.24262688X-RAY DIFFRACTION99
4.0635-4.47210.23731580.17392708X-RAY DIFFRACTION99
4.4721-5.11840.25741450.16042732X-RAY DIFFRACTION99
5.1184-6.44570.271520.20492778X-RAY DIFFRACTION99
6.4457-45.20470.22661530.17722941X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.22270.13330.11010.14640.11120.08290.21730.0154-0.45140.07140.0614-0.11990.1726-0.09980.29950.06090.2747-0.07630.270.16960.4656-0.0988-59.1393-7.3227
20.02580.00360.02670.056-0.01170.05-0.0965-0.0313-0.02420.0552-0.003-0.1142-0.0299-0.0075-0.04450.21620.13820.03170.18780.11360.446720.0249-32.2992-28.0656
30.0405-0.06740.02020.0879-0.01420.06980.0472-0.0638-0.0195-0.01580.0618-0.09940.0142-0.06330.2460.03710.13870.02670.12270.01180.08661.3383-38.3655-15.9858
40.1864-0.01690.11710.1576-0.16370.2303-0.0118-0.43480.04070.1932-0.2133-0.0828-0.4419-0.1738-0.8010.10290.4665-0.1901-0.1760.5032-0.19667.1911-26.627214.9766
50.0625-0.01280.0190.0009-0.00410.0120.04990.1758-0.07070.0504-0.023-0.02750.02280.0232-0.00620.34590.0395-0.00030.37610.09670.22864.2929-27.7765-2.7276
60.00750.0014-0.00480.0129-0.01320.02080.03890.0338-0.006-0.0367-0.03230.0021-0.0006-0.0035-0.01420.650.37450.01640.72790.33010.732415.8062-44.9553-1.4914
70.00050.0006-0.00040.00130.00150.00460.01350.0082-0.003-0.010.00970.0048-0.00250.002600.87-0.15980.01120.7170.02190.730511.0895-58.21686.6243
80.1179-0.072-0.05710.1834-0.03180.1058-0.05490.03780.01580.0126-0.021-0.04060.0629-0.0685-0.02440.66320.1502-0.11120.43080.12450.356730.305-41.102-23.39
90.0088-0.00750.00790.0081-0.00770.00860.0021-0.02270.0023-0.0107-0.009-0.0041-0.0140.002100.3513-0.01-0.0080.4135-0.18430.34315.13-33.708-2.073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 174 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 175 THROUGH 229 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 230 THROUGH 315 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 316 THROUGH 685 )
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 1 THROUGH 10 )
6X-RAY DIFFRACTION6CHAIN 'E' AND (RESID 11 THROUGH 15 )
7X-RAY DIFFRACTION7CHAIN 'E' AND (RESID 16 THROUGH 17 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 19 THROUGH 21 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 4 THROUGH 18 )

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