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- PDB-6xup: Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-... -

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Basic information

Entry
Database: PDB / ID: 6xup
TitleArchaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT
Components
  • 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
  • Piwi protein
KeywordsDNA BINDING PROTEIN / ARGONAUTE / PIWI DOMAIN / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


nucleic acid binding / 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 / CACODYLATE ION / : / DNA / DNA (> 10) / Piwi protein / Piwi protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsGrazulis, S. / Zaremba, M.
CitationJournal: To be published
Title: Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT
Authors: Golovinas, E. / Manakova, E. / Sasnauskas, G. / Zaremba, M.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 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
R: 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
S: 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
B: Piwi protein
P: 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
Q: 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,57827
Polymers118,9656
Non-polymers1,61321
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-76 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.798, 60.872, 101.718
Angle α, β, γ (deg.)76.560, 75.590, 79.390
Int Tables number1
Space group name H-MP1

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Components

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Protein / DNA chain , 2 types, 6 molecules ABRSPQ

#1: Protein Piwi protein /


Mass: 50921.121 Da / Num. of mol.: 2 / Fragment: Arhaeoglobus fulgidus Argonaute protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A101DYI0, UniProt: O28951*PLUS
#2: DNA chain
5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'


Mass: 4280.792 Da / Num. of mol.: 4 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 7 types, 470 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-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Na-Cacodylate pH 5.5 0.05 M, KCl 0.12 M, MgCl2 0.01 M, PEG3350 7%, DTT_0.005 M, glycerol 5% (w/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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→41.5 Å / Num. obs: 91396 / % possible obs: 91.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.943.90.95545560.6290.5571.10691.2
9.87-41.53.50.035720.9970.0190.03687.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.498
Highest resolutionLowest resolution
Rotation40.72 Å2.35 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
pointless1.10.26data scaling
Aimless0.5.27data scaling
MOLREP11.6.04phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2w42

2w42


Resolution: 1.9→40.716 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2243 8344 10.03 %
Rwork0.1813 --
obs0.1856 83692 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.04 Å2 / Biso mean: 48.8122 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 1.9→40.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 516 85 449 7569
Biso mean--65.73 53.04 -
Num. residues----828
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.39645850.3727492891
1.9216-1.94420.33994960.3291488590
1.9442-1.96790.34075360.3147503290
1.9679-1.99280.33845700.3008500990
1.9928-2.01910.30595060.2817484889
2.0191-2.04670.28474990.2678496090
2.0467-2.0760.28215940.2484495090
2.076-2.10690.28215330.2406494490
2.1069-2.13990.28875060.2294492290
2.1399-2.17490.26056220.2229492090
2.1749-2.21240.25115840.2115481889
2.2124-2.25270.2515600.2012498089
2.2527-2.2960.25895210.2101479190
2.296-2.34290.2546310.2013493590
2.3429-2.39380.25925340.2012482590
2.3938-2.44950.26015860.21487789
2.4495-2.51070.26295620.2025493190
2.5107-2.57860.26425510.1985509892
2.5786-2.65450.2565380.2052498691
2.6545-2.74010.25015390.1975513293
2.7401-2.8380.24596120.1928495492
2.838-2.95160.26045720.1945500592
2.9516-3.08590.22365590.1869509692
3.0859-3.24850.25045870.1883500992
3.2485-3.4520.19785540.1633500191
3.452-3.71830.19915360.1623498791
3.7183-4.09220.18855650.1493492590
4.0922-4.68360.16024840.1278497989
4.6836-5.8980.18855540.1458520895
5.898-40.7160.20545410.1763507692

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