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- PDB-6d9l: Ternary RsAgo Complex with Guide RNA and Target DNA Containing G-... -

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Basic information

Entry
Database: PDB / ID: 6d9l
TitleTernary RsAgo Complex with Guide RNA and Target DNA Containing G-A Non-canonical Pair
Components
  • DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')
  • RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
  • Uncharacterized protein
KeywordsRNA BINDING PROTEIN/RNA/DNA / guide RNA. target DNA. RNA-DNA heteroduplex. non-canonical base pairs and bulges / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


clearance of foreign intracellular DNA / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
Rhodobacter sphaeroides ATCC 17025 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLiu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2018
Title: Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.
Authors: Liu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Kulbachinskiy, A. / Aravin, A.A. / Patel, D.J.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
C: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')
F: Uncharacterized protein
H: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
J: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,3948
Polymers204,3456
Non-polymers492
Water2,504139
1
A: Uncharacterized protein
C: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1974
Polymers102,1733
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-64 kcal/mol
Surface area33700 Å2
MethodPISA
2
F: Uncharacterized protein
H: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
J: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1974
Polymers102,1733
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-62 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.045, 118.253, 117.827
Angle α, β, γ (deg.)90.000, 95.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 89038.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) (bacteria)
Strain: ATCC 17025 / ATH 2.4.3 / Gene: Rsph17025_3694 / Production host: Escherichia coli (E. coli) / References: UniProt: A4WYU7
#2: RNA chain RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')


Mass: 5788.491 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)
#3: DNA chain DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')


Mass: 7345.742 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% MPD, 30 mM magnesium acetate, 50 mM sodium cacodylate pH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 55738 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.722 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→41.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.342 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 2824 5.1 %RANDOM
Rwork0.2117 ---
obs0.2138 52883 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.22 Å2 / Biso mean: 51.726 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å2-0.53 Å2
2--4.82 Å20 Å2
3----2.55 Å2
Refinement stepCycle: final / Resolution: 2.6→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11607 1570 2 139 13318
Biso mean--37.21 42.83 -
Num. residues----1591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01813616
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212004
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.85518849
X-RAY DIFFRACTIONr_angle_other_deg0.783327493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61751514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08322.611517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.246151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.64815109
X-RAY DIFFRACTIONr_chiral_restr0.0560.22085
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023218
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 216 -
Rwork0.271 3590 -
all-3806 -
obs--90.73 %

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