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- PDB-5gq9: Crystal structure of Thermus thermophilus Argonaute in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5gq9
TitleCrystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target
Components
  • DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • Thermus thermophilus Argonaute
KeywordsDNA BINDING PROTEIN/DNA / Argonaute / Complex / Guide DNA / DNA BINDING PROTEIN-DNA complex
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
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / 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: 2.7 Å
AuthorsZhao, H. / Sheng, G. / Wang, Y.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China91440201 China
National Natural Science Foundation of China31571335 China
National Natural Science Foundation of China31400640 China
Ministry of Science and Technology (China)2014CB910102 China
Strategic Priority Research program of the Chinese Academy of SciencesXDB08010203 China
CitationJournal: To Be Published
Title: Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target
Authors: Zhao, H. / Sheng, G. / Wang, Y.
History
DepositionAug 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support / struct
Item: _entity.pdbx_description / _pdbx_audit_support.funding_organization / _struct.pdbx_descriptor
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Thermus thermophilus Argonaute
C: DNA (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
D: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
B: Thermus thermophilus Argonaute
E: DNA (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,32412
Polymers176,1786
Non-polymers1466
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20230 Å2
ΔGint-135 kcal/mol
Surface area56760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.831, 116.503, 161.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thermus thermophilus Argonaute


Mass: 76728.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some residues are missing due to disorder in the coordinate.
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 (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q746M7
#2: DNA chain DNA (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')


Mass: 6573.254 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The last five nucleotides are missing due to disorder.
Source: (synth.) Thermus thermophilus (bacteria)
#3: DNA chain DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')


Mass: 4787.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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: 2.99 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium acetate, 0.1M Bis-tris Propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97848 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 58404 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rsym value: 0.066 / Net I/σ(I): 21.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.45 / % possible all: 99.5

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Processing

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

4ncb


Resolution: 2.7→39.13 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.2366 3022 5.18 %
Rwork0.1893 --
obs0.1919 58339 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10281 1314 6 0 11601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912003
X-RAY DIFFRACTIONf_angle_d1.3116562
X-RAY DIFFRACTIONf_dihedral_angle_d18.4774580
X-RAY DIFFRACTIONf_chiral_restr0.0781819
X-RAY DIFFRACTIONf_plane_restr0.0061932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6964-2.73860.34171090.29022399X-RAY DIFFRACTION96
2.7386-2.78340.33051080.2772530X-RAY DIFFRACTION100
2.7834-2.83140.36861260.25942474X-RAY DIFFRACTION99
2.8314-2.88290.32231380.25422502X-RAY DIFFRACTION99
2.8829-2.93830.31061370.24652476X-RAY DIFFRACTION100
2.9383-2.99830.30021310.23732476X-RAY DIFFRACTION99
2.9983-3.06350.28021320.23762497X-RAY DIFFRACTION100
3.0635-3.13470.29911430.21142478X-RAY DIFFRACTION100
3.1347-3.2130.25281260.19692522X-RAY DIFFRACTION100
3.213-3.29990.26321120.19832514X-RAY DIFFRACTION100
3.2999-3.39690.2691330.19882511X-RAY DIFFRACTION100
3.3969-3.50650.2841700.20192485X-RAY DIFFRACTION100
3.5065-3.63170.23541460.19492489X-RAY DIFFRACTION100
3.6317-3.7770.2411510.18522487X-RAY DIFFRACTION100
3.777-3.94880.24671320.17852513X-RAY DIFFRACTION100
3.9488-4.15670.22761350.17282537X-RAY DIFFRACTION100
4.1567-4.41680.24261180.16332519X-RAY DIFFRACTION100
4.4168-4.75730.17911410.15262567X-RAY DIFFRACTION100
4.7573-5.23510.19011390.16572543X-RAY DIFFRACTION100
5.2351-5.99030.23321810.18472526X-RAY DIFFRACTION100
5.9903-7.53830.22991510.19652582X-RAY DIFFRACTION100
7.5383-39.13370.19861630.17952690X-RAY DIFFRACTION99

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