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- PDB-7r8h: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound... -

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Basic information

Entry
Database: PDB / ID: 7r8h
TitleCrystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA
Components
  • Argonaute
  • DNA (5'-D(*TP*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: 2.54 Å
AuthorsShin, Y. / Murakami, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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*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)93,4552
Polymers93,4552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-22 kcal/mol
Surface area35510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.823, 199.823, 199.823
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: 87914.734 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*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)-3')


Mass: 5540.604 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl, pH 8.0, 8% PEG 8,000

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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: 2.54→50 Å / Num. obs: 43544 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 78.84 Å2 / CC1/2: 1 / Rpim(I) all: 0.027 / Net I/σ(I): 28.8
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2179 / CC1/2: 0.32 / Χ2: 1.095 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.54→44.68 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 1993 4.61 %
Rwork0.2003 41278 -
obs0.202 43271 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.39 Å2
Refinement stepCycle: LAST / Resolution: 2.54→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 372 0 0 6408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096588
X-RAY DIFFRACTIONf_angle_d1.09648988
X-RAY DIFFRACTIONf_chiral_restr0.0599979
X-RAY DIFFRACTIONf_plane_restr0.00971114
X-RAY DIFFRACTIONf_dihedral_angle_d20.35862508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.610.46361360.3952913X-RAY DIFFRACTION98.9
2.61-2.680.43241400.34262881X-RAY DIFFRACTION98.31
2.68-2.760.33961400.31322918X-RAY DIFFRACTION98.9
2.76-2.850.35571420.2922900X-RAY DIFFRACTION98.64
2.85-2.950.33721440.28972902X-RAY DIFFRACTION99.06
2.95-3.070.32821370.28112950X-RAY DIFFRACTION99.39
3.07-3.20.33561420.30952933X-RAY DIFFRACTION99.61
3.21-3.370.27251440.24862934X-RAY DIFFRACTION99.87
3.37-3.580.28861410.23562960X-RAY DIFFRACTION99.94
3.59-3.860.2731440.20772967X-RAY DIFFRACTION99.81
3.86-4.250.22531420.19352952X-RAY DIFFRACTION99.77
4.25-4.860.16691430.15582986X-RAY DIFFRACTION100
4.87-6.130.17871470.18123005X-RAY DIFFRACTION100
6.13-44.680.21021510.14373077X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.04308217405-1.462090010760.4741209518461.85892333899-0.1841569860181.89907190465-0.11229301605-0.120030548667-0.6588140256760.1062708985960.06969651803440.4386836660580.508281762185-0.08852314888430.05186407977180.7954827169990.1205929187580.1828618091420.439129294050.03289091089710.68164044653432.92363060596.2846043789867.525198837
21.60561728801-0.6372220232721.017079312942.34046815191-1.812038459174.97702762251-0.1195412729060.08710902465290.0255874882495-0.119448292329-0.147745379655-0.1653219519220.2545953820880.2544030852530.2507431811530.4327937236050.02327644836930.1097486386590.4732130302420.04789246313620.60421146666670.48730818312.6687550837343.8916752396
32.65289153654-1.43333149016-0.6612594945885.105937112812.283442813943.73533228258-0.04503523110360.230448281614-0.2706768252960.39874687505-0.4865067723440.6272235414990.255424407811-0.9513150762820.4862760906550.4455513457430.04505118175930.1422967494220.779258364344-0.08001511099770.52638478585458.3833309408-8.5475232581563.5920917502
43.976540977380.602853949506-2.883985646790.289010504093-0.5059485205692.44170631973-0.3811325537640.3892911889210.253412757821-0.00525582749518-0.2004420903830.332835002383-0.625297643262-0.7107861159060.3642559553270.7394216750150.3339950110110.1158633849030.774300097935-0.005342121174070.7390468321554.00158003098.980988227456.5776780982
50.09215204677730.1782225907070.01888968119750.374814451379-0.04980118217480.2790883456710.5211450108740.763181704241-0.547137596845-0.432685300886-0.620596003647-0.5327685358591.418853364511.05830546369-0.04524522683931.478942070020.3616001249780.1797720957691.070772079570.200605689331.6322137184230.51018326552.201151780663.7071637727
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 340 )AA1 - 3401 - 340
22chain 'A' and (resid 341 through 557 )AA341 - 557341 - 557
33chain 'A' and (resid 558 through 769 )AA558 - 769558 - 769
44chain 'T' and (resid 1 through 10 )TB1 - 10
55chain 'T' and (resid 11 through 18 )TB11 - 18

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