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- PDB-7r8k: Crystal structure of Pseudooceanicola lipolyticus Argonaute (SeMe... -

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Basic information

Entry
Database: PDB / ID: 7r8k
TitleCrystal structure of Pseudooceanicola lipolyticus Argonaute (SeMet labeled protein)
ComponentsArgonaute
KeywordsHYDROLASE / argonaute / Ago / DNA guide / RNA cleavage
Function / homologyRibonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Piwi domain-containing protein
Function and homology information
Biological speciesPseudooceanicola lipolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.28 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 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)89,1551
Polymers89,1551
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)199.813, 199.813, 199.813
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: 89155.148 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
Has ligand of interestN
Has protein modificationY

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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: 3.73 Å3/Da / Density % sol: 67.01 %
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: 0.9717 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 3.28→50 Å / Num. obs: 19786 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.997 / Rpim(I) all: 0.029 / Net I/σ(I): 23.7
Reflection shellResolution: 3.5→3.56 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 867 / CC1/2: 0.699 / Rpim(I) all: 0.387 / Χ2: 0.885 / % 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: 3.28→47.1 Å / SU ML: 0.494 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.1401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2654 1930 9.75 %
Rwork0.2204 17856 -
obs0.2248 19786 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.86 Å2
Refinement stepCycle: LAST / Resolution: 3.28→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 0 0 6029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01266164
X-RAY DIFFRACTIONf_angle_d1.70168337
X-RAY DIFFRACTIONf_chiral_restr0.0745909
X-RAY DIFFRACTIONf_plane_restr0.01351093
X-RAY DIFFRACTIONf_dihedral_angle_d9.2665843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.360.38831180.37341177X-RAY DIFFRACTION89.13
3.36-3.450.41641340.34961205X-RAY DIFFRACTION92.28
3.46-3.560.38561360.32211220X-RAY DIFFRACTION94.43
3.56-3.670.33261320.28511244X-RAY DIFFRACTION94.83
3.67-3.80.34111320.27341244X-RAY DIFFRACTION96.63
3.8-3.950.29511350.25361275X-RAY DIFFRACTION96.58
3.96-4.130.29441390.22551258X-RAY DIFFRACTION97.01
4.14-4.350.23471440.22891282X-RAY DIFFRACTION98.34
4.35-4.620.25521370.20661287X-RAY DIFFRACTION98.34
4.63-4.980.25941380.21481306X-RAY DIFFRACTION98.84
4.98-5.480.30091440.2261308X-RAY DIFFRACTION99.52
5.48-6.270.32041390.24111332X-RAY DIFFRACTION99.86
6.27-7.90.28671500.24071339X-RAY DIFFRACTION99.8
7.91-47.10.18611520.15491379X-RAY DIFFRACTION100

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