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- PDB-7r8g: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound... -

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Basic information

Entry
Database: PDB / ID: 7r8g
TitleCrystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA
Components
  • Argonaute
  • DNA (5'-D(*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)-3')
KeywordsHYDROLASE/DNA / Argonaute / Ago / DNA guide / RNA cleavage / HYDROLASE-DNA complex
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
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) / Piwi domain-containing protein
Similarity search - Component
Biological speciesPseudooceanicola lipolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShin, Y. / Murakami, K.S.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Nat Commun / Year: 2022
Title: Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity.
Authors: Lisitskaya, L. / Shin, Y. / Agapov, A. / Olina, A. / Kropocheva, E. / Ryazansky, S. / Aravin, A.A. / Esyunina, D. / Murakami, K.S. / Kulbachinskiy, A.
History
DepositionJun 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argonaute
T: DNA (5'-D(*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)93,2752
Polymers93,2752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-13 kcal/mol
Surface area35530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.598, 200.598, 200.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Argonaute


Mass: 88038.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudooceanicola lipolyticus (bacteria)
Gene: CVM52_05730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2M8J4C7
#2: DNA chain DNA (5'-D(*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)-3')


Mass: 5236.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudooceanicola lipolyticus (bacteria)

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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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 8.0, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 46475 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 75.05 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 27.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2292 / CC1/2: 0.344 / Rpim(I) all: 0.944 / Χ2: 1.16 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.86 Å / SU ML: 0.4161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2541 2003 4.31 %
Rwork0.2109 44461 -
obs0.2128 46464 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 307 0 0 6336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876506
X-RAY DIFFRACTIONf_angle_d1.0838861
X-RAY DIFFRACTIONf_chiral_restr0.0583970
X-RAY DIFFRACTIONf_plane_restr0.00951109
X-RAY DIFFRACTIONf_dihedral_angle_d18.37542469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.38291430.33623166X-RAY DIFFRACTION99.88
2.56-2.630.34821390.31573121X-RAY DIFFRACTION99.97
2.63-2.710.37761410.34333153X-RAY DIFFRACTION100
2.71-2.790.36731450.32133164X-RAY DIFFRACTION100
2.79-2.890.32411410.31883180X-RAY DIFFRACTION99.94
2.89-3.010.36381430.28643129X-RAY DIFFRACTION100
3.01-3.150.37091430.29653162X-RAY DIFFRACTION100
3.15-3.310.33931430.27423165X-RAY DIFFRACTION100
3.31-3.520.35121390.26533153X-RAY DIFFRACTION100
3.52-3.790.27911460.21733192X-RAY DIFFRACTION99.97
3.79-4.170.25551430.20753185X-RAY DIFFRACTION100
4.18-4.780.22851420.1673192X-RAY DIFFRACTION100
4.78-6.020.22151440.18313206X-RAY DIFFRACTION99.97
6.02-44.860.1641510.1543293X-RAY DIFFRACTION99.83

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