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- PDB-4n47: Structure of Thermus thermophilus Argonaute bound to guide DNA an... -

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Basic information

Entry
Database: PDB / ID: 4n47
TitleStructure of Thermus thermophilus Argonaute bound to guide DNA and 12-mer target DNA
Components
  • 5'-D(*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
  • 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
  • Argonaute
KeywordsNUCLEAR PROTEIN/DNA / Argonaute / RNA interference / DNA interference / NUCLEAR 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 / Argonaute, N-terminal domain / Argonaute, middle domain / Piwi domain profile. / Piwi domain ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / 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 / molecular replacement / Resolution: 2.823 Å
AuthorsSheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Wang, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Authors: Sheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Tian, W. / Swarts, D.C. / van der Oost, J. / Patel, D.J. / Wang, Y.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,9004
Polymers86,8753
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-42 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.886, 110.548, 124.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Argonaute


Mass: 76728.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: Thermophilus / Gene: Argonaute, TT_P0026 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q746M7
#2: DNA chain 5'-D(*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'


Mass: 3558.331 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'


Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 306K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19791 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 66.14 Å2 / Rmerge(I) obs: 0.096 / Χ2: 1.512 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.856.10.6129691.175199.8
2.85-2.960.5559921.2311100
2.9-2.966.10.469781.181199.8
2.96-3.026.10.389711.155199.9
3.02-3.0860.3259731.3631100
3.08-3.1560.2619751.288199.7
3.15-3.2360.19810021.4571100
3.23-3.3260.1679641.594199.5
3.32-3.4260.1429871.5261100
3.42-3.5360.1359681.728199.7
3.53-3.6560.119931.532199.4
3.65-3.860.1059881.662199.7
3.8-3.975.90.1059761.838199.9
3.97-4.185.90.09110041.867199.7
4.18-4.445.90.08610051.668199.8
4.44-4.795.80.0889901.818199.7
4.79-5.275.80.08410101.808199.4
5.27-6.035.60.0810011.655199.5
6.03-7.595.60.06810271.497198.3
7.59-505.70.05210181.234191.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F73

3f73


Resolution: 2.823→38.329 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1004 5.09 %RANDOM
Rwork0.1921 ---
obs0.1957 19727 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.31 Å2 / Biso mean: 66.2182 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.823→38.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 533 1 0 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085729
X-RAY DIFFRACTIONf_angle_d1.017910
X-RAY DIFFRACTIONf_chiral_restr0.057885
X-RAY DIFFRACTIONf_plane_restr0.004942
X-RAY DIFFRACTIONf_dihedral_angle_d17.1922085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.823-2.97160.31561190.2492473259292
2.9716-3.15770.38921400.253926602800100
3.1577-3.40130.30721480.2126762824100
3.4013-3.74340.27271660.194226772843100
3.7434-4.28440.24081500.177127172867100
4.2844-5.39550.21471440.169427412885100
5.3955-38.33230.26061370.18852779291696
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)
11.6581-0.36020.82241.7624-2.11254.2798-0.02190.3288-0.0444-0.09620.20450.1566-0.0134-0.823-0.09850.51940.0959-0.0090.3656-0.03120.3748-27.302422.74790.8991
24.5863-3.00311.83681.74-1.07581.25190.08520.16040.37470.0696-0.1593-0.1745-0.1248-0.18660.06350.4136-0.0994-0.01480.33850.07290.3034-14.173319.197514.4565
32.3216-0.2241-1.43751.0989-0.63475.2679-0.03270.7385-0.2256-0.22520.16180.01660.36990.2149-0.17070.538-0.1197-0.01770.4724-0.0520.56426.45917.0513-2.6961
41.7797-1.6375-0.05524.4049-0.50881.4513-0.2197-0.1455-0.43650.30870.10040.2250.27990.08560.13040.3463-0.01530.05280.48520.05290.3063-12.5316-17.000928.6051
52.0154-0.53050.67782.94390.23653.6932-0.0710.2429-0.0775-0.2247-0.12880.34750.26680.19620.15330.4965-0.09620.06360.39940.04360.4111-14.3694-22.446619.36
61.8887-0.38990.72782.83330.48313.7729-0.2685-0.0487-0.1331-0.2440.11850.9614-0.2117-0.61520.15010.2406-0.0717-0.090.5270.0770.7559-30.1424-8.506521.6472
72.9739-1.912-0.25215.29870.50514.71390.30170.3825-1.0332-1.2791-0.27880.44940.7412-0.0463-0.00860.7818-0.1852-0.10030.64570.00380.6871-18.6295-22.41714.1063
82.16940.5993-1.06710.3681-0.94612.0523-0.14690.1506-0.2559-0.0485-0.1169-0.1691-0.3087-0.03590.1530.5739-0.0572-0.09720.54960.06960.5172-8.5141-4.200420.5125
91.13280.564-1.08093.281-1.14660.9634-0.17010.44780.1882-0.4860.41270.40020.13830.0857-0.16840.5202-0.0702-0.06720.44160.11240.5013-9.4078-2.253116.9272
103.8958-1.49-0.33834.7448-2.21595.69470.60140.9957-1.0162-1.3644-0.51321.21470.6712-1.40650.54310.6538-0.0132-0.02631.1543-0.54991.0441-0.55295.7765-13.3361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 102 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 175 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 282 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 401 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 514 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 515 through 653 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 654 through 685 )A0
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 12 )D0
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 12 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 20 through 21 )C0

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