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- PDB-6t5t: Crystal structure of Archaeoglobus fulgidus Argonaute protein wit... -

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Basic information

Entry
Database: PDB / ID: 6t5t
TitleCrystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTGGCCACAAT
Components
  • 5'-D(*AP*TP*TP*GP*TP*GP*GP*CP*CP*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 / Piwi domain profile. / Piwi domain / Piwi / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / 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: 1.7003 Å
AuthorsGrazulis, S. / Zaremba, M.
CitationJournal: To be published
Title: Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTGGCCACAAT
Authors: Golovinas, E. / Manakova, E. / Sasnauskas, G. / Zaremba, M.
History
DepositionOct 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: 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*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'
S: 5'-D(*AP*TP*TP*GP*TP*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,17516
Polymers59,4813
Non-polymers69413
Water5,729318
1
A: Piwi protein AF_1318
R: 5'-D(*AP*TP*TP*GP*TP*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'
S: 5'-D(*AP*TP*TP*GP*TP*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)120,35032
Polymers118,9616
Non-polymers1,38926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area12350 Å2
ΔGint-119 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.098, 99.551, 109.901
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-505-

K

21A-895-

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: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
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*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'


Mass: 4279.804 Da / Num. of mol.: 2 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 5 types, 331 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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 % / Mosaicity: 0.12 °
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
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.7→99.551 Å / Num. all: 63695 / Num. obs: 63695 / % possible obs: 100 % / Redundancy: 10.3 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Rsym value: 0.063 / Net I/av σ(I): 4.3 / Net I/σ(I): 20.8 / Num. measured all: 657679
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.7910.10.9690.89322591920.3351.0750.9692.3100
1.79-1.910.60.5081.59147286690.1720.5610.5084.3100
1.9-2.0310.60.2742.78702582020.0920.3020.2747.6100
2.03-2.19100.1594.57641676280.0550.1750.15912100
2.19-2.410.80.1056.47593770450.0340.1140.10518.1100
2.4-2.6910.50.0817.56725464010.0270.0880.08124.2100
2.69-3.110.30.0657.45842856800.0210.070.06534.9100
3.1-3.810.30.0548.24979448520.0170.0580.05451.6100
3.8-5.389.90.04211.13759738040.0130.0450.04263.7100
5.38-99.5519.20.0477.32053122220.0160.0520.04761.199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.569
Highest resolutionLowest resolution
Rotation54.95 Å2.24 Å
Translation54.95 Å2.24 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
SCALA3.3.22data scaling
MOLREPVers 11.6.04; 25.05.2018phasing
PHENIX1.13refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ytu

1ytu


Resolution: 1.7003→54.9506 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 11898 9.81 %Test (R-free flags) flag value: 0
Rwork0.1805 ---
obs-121243 99.823 %-
Displacement parametersBiso max: 136.66 Å2 / Biso mean: 42.7955 Å2 / Biso min: 15.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7003→54.9506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 576 31 318 4198

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