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- PDB-6xu0: Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-... -

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Basic information

Entry
Database: PDB / ID: 6xu0
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 17, 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
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)119,92517
Polymers118,9656
Non-polymers95911
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-55 kcal/mol
Surface area35910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.909, 61.205, 103.092
Angle α, β, γ (deg.)98.320, 104.960, 100.620
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) / Gene: XD48_2091 / 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, 459 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#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.: 448 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Na-Cacodylate pH 6.5 0.05 M, KCl_0.04 M, MgCl2 0.01 M, PEG3350 11% (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→48.785 Å / Num. obs: 85105 / % possible obs: 91.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.03 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.079 / Rsym value: 0.061 / Net I/av σ(I): 7.1 / Net I/σ(I): 8.3
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
1.9-23.90.6381.248635123550.4490.8940.6381.790.9
2-2.123.90.371245876116580.2580.5150.3712.790.9
2.12-2.273.90.2273.243309110110.1570.3130.227490.6
2.27-2.453.90.154.940547102910.1020.2040.155.491.8
2.45-2.693.90.1066.83753395260.0720.1430.1067.292.2
2.69-33.90.07793359785560.0510.1010.0771091.5
3-3.473.90.05711.72919974910.0370.0730.05714.790.8
3.47-4.2540.04714.22558364760.0290.0580.04719.593.1
4.25-6.013.90.0415.21963249720.0250.0490.0421.392.5
6.01-48.7853.90.038121088827690.0250.0490.03821.794

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.26 Å48.78 Å
Translation2.26 Å48.78 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ytu

1ytu


Resolution: 1.9→46.439 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2252 8390 9.97 %
Rwork0.1805 --
obs0.1849 84166 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.34 Å2 / Biso mean: 46.915 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 1.9→46.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 557 46 448 7562
Biso mean--76.32 49.23 -
Num. residues----830
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.34535730.3216497190
1.9216-1.94420.35095910.3064492290
1.9442-1.96790.32225670.2948504189
1.9679-1.99280.31125900.274500890
1.9928-2.01910.29965430.2693497689
2.0191-2.04670.29465380.2524499890
2.0467-2.0760.28965150.2425513790
2.076-2.1070.2825660.2412500690
2.107-2.13990.27755530.234496790
2.1399-2.1750.30025840.2249500989
2.175-2.21250.26975310.2113489989
2.2125-2.25270.22685830.1987509889
2.2527-2.2960.26145430.2081498490
2.296-2.34290.26245950.1967515891
2.3429-2.39380.27565640.194497191
2.3938-2.44950.25255600.1964512691
2.4495-2.51080.28055710.1939507092
2.5108-2.57860.26954980.1964521992
2.5786-2.65450.26425070.1978511591
2.6545-2.74020.25375350.196508691
2.7402-2.83810.26625700.1958494390
2.8381-2.95170.25575950.1921511791
2.9517-3.0860.22545930.1744495690
3.086-3.24870.21595820.1825497289
3.2487-3.45220.2055680.1613506391
3.4522-3.71860.20365100.1636507791
3.7186-4.09260.18585370.1489528593
4.0926-4.68440.1585640.1272517192
4.6844-5.89990.19555400.1484508491
5.8999-46.4390.20376140.1858512393

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