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- PDB-6tuo: Crystal structure of Archaeoglobus fulgidus Argonaute protein wit... -

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Basic information

Entry
Database: PDB / ID: 6tuo
TitleCrystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT
Components
  • 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
  • Piwi protein AF_1318
KeywordsDNA BINDING PROTEIN / ARGONAUTE / PIWI DOMAIN / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Piwi protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGrazulis, S. / Zaremba, M.
CitationJournal: To be published
Title: Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT
Authors: Golovinas, E. / Manakova, E. / Sasnauskas, G. / Zaremba, M.
History
DepositionJan 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Piwi protein AF_1318
R: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
S: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,24713
Polymers59,4793
Non-polymers76910
Water6,305350
1
A: Piwi protein AF_1318
R: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
S: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
hetero molecules

A: Piwi protein AF_1318
R: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
S: 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,49526
Polymers118,9586
Non-polymers1,53720
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area13800 Å2
ΔGint-79 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.011, 99.634, 109.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

21A-926-

HOH

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Components

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Protein / DNA chain , 2 types, 3 molecules ARS

#1: Protein Piwi protein AF_1318 / AfAgo / AfPiwi / PIWI/MID domain protein


Mass: 50921.121 Da / Num. of mol.: 1 / Fragment: Arhaeoglobus fulgidus Argonaute protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: DSM 4304 / Gene: AF_1318 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O28951
#2: DNA chain 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'


Mass: 4278.815 Da / Num. of mol.: 2 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 6 types, 360 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Na-Cacodylate pH 5.5 0.05 M, KCl_0.2 M, MgCl2 0.01 M, PEG4000 5% (w/v), glycerol 5% (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2018 / Details: silica substrate + Rh coating
RadiationMonochromator: Oxford-FMB, UK; Si(111) or Si(311); both crystals LN2 cooled, fixed exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.8→99.63 Å / Num. all: 349485 / Num. obs: 53664 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.846.70.8152100531280.90.3370.8832.6100
9-99.635.60.02728945140.9980.0130.0360.999

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.461
Highest resolutionLowest resolution
Rotation54.9 Å2.23 Å
Translation54.9 Å2.23 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
MOLREP11.6.04; 25.05.2018phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ytu

1ytu


Resolution: 1.8→54.901 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 27.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 5287 9.84 %Random selection
Rwork0.1841 ---
obs0.1883 53664 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.13 Å2 / Biso mean: 48.285 Å2 / Biso min: 15.24 Å2
Refinement stepCycle: final / Resolution: 1.8→54.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 576 44 350 4264
Biso mean--58.16 49.87 -
Num. residues----433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.41583470.3708302099
1.8205-1.84190.36323500.33883054100
1.8419-1.86430.34853300.3263054100
1.8643-1.8880.3333150.29643072100
1.888-1.91280.33243510.28993058100
1.9128-1.9390.29543370.26843055100
1.939-1.96670.32523240.26263048100
1.9667-1.99610.28183530.24373081100
1.9961-2.02720.30092990.22983044100
2.0272-2.06050.27263100.22593092100
2.0605-2.0960.26153260.20613115100
2.096-2.13410.24093510.20253001100
2.1341-2.17520.27683180.19823130100
2.1752-2.21960.25793520.18973021100
2.2196-2.26780.23023480.1923018100
2.2678-2.32060.2433530.19243068100
2.3206-2.37860.21163340.17893047100
2.3786-2.44290.223560.18593063100
2.4429-2.51480.24383110.19943055100
2.5148-2.5960.27383280.18893110100
2.596-2.68880.27563800.193007100
2.6888-2.79640.26513340.19573076100
2.7964-2.92370.21943030.18763081100
2.9237-3.07780.25423280.18673097100
3.0778-3.27060.22483260.19253053100
3.2706-3.52310.23593100.16953087100
3.5231-3.87760.18493320.15183063100
3.8776-4.43850.16723620.1396300599
4.4385-5.59120.17613350.14323086100
5.5912-100.20713200.1787306199

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