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- PDB-7r8f: Crystal structure of Pseudooceanicola lipolyticus Argonaute -

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Basic information

Entry
Database: PDB / ID: 7r8f
TitleCrystal structure of Pseudooceanicola lipolyticus Argonaute
ComponentsArgonaute
KeywordsHYDROLASE / argonaute / Ago / DNA guide / RNA cleavage
Function / homologyRibonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta / Piwi domain-containing protein
Function and homology information
Biological speciesPseudooceanicola lipolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.16 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

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Assembly

Deposited unit
A: Argonaute


Theoretical massNumber of molelcules
Total (without water)88,0391
Polymers88,0391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.938, 197.938, 197.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
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

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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: 3.77 Å3/Da / Density % sol: 67.39 %
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: 0.9687 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 23413 / % possible obs: 100 % / Redundancy: 18.2 % / Rpim(I) all: 0.07 / Χ2: 1.761 / Net I/σ(I): 24
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 2310 / CC1/2: 0.331 / Χ2: 1.051 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.16→49.48 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1999 8.95 %
Rwork0.2144 --
obs0.2185 22325 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6019 0 0 0 6019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126144
X-RAY DIFFRACTIONf_angle_d1.6948309
X-RAY DIFFRACTIONf_dihedral_angle_d18.3552319
X-RAY DIFFRACTIONf_chiral_restr0.093904
X-RAY DIFFRACTIONf_plane_restr0.0151090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.230.42641410.3491424X-RAY DIFFRACTION100
3.23-3.320.3431420.30671452X-RAY DIFFRACTION100
3.32-3.420.31771370.27861435X-RAY DIFFRACTION100
3.42-3.530.28731450.26571451X-RAY DIFFRACTION100
3.53-3.650.29261440.2581428X-RAY DIFFRACTION100
3.66-3.80.29091420.27371436X-RAY DIFFRACTION100
3.8-3.970.32431390.23931440X-RAY DIFFRACTION100
3.98-4.180.28621430.22211459X-RAY DIFFRACTION100
4.19-4.450.23781440.20511440X-RAY DIFFRACTION100
4.45-4.790.25511400.20971431X-RAY DIFFRACTION100
4.79-5.270.24851450.20331464X-RAY DIFFRACTION100
5.27-6.030.28541420.21841460X-RAY DIFFRACTION100
6.03-7.590.25331420.22291485X-RAY DIFFRACTION100
7.6-49.480.18561530.14841521X-RAY DIFFRACTION100

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