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- PDB-8rzf: RNase W from Sulfolobus acidocaldarius -

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Basic information

Entry
Database: PDB / ID: 8rzf
TitleRNase W from Sulfolobus acidocaldarius
ComponentsProbable ribonuclease FAU-1
KeywordsHYDROLASE / Ribonuclease / FAU-1 / Archaea / Ribosome biogenesis
Function / homology
Function and homology information


RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / rRNA processing
Similarity search - Function
RNA-binding FAU-1 / : / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402)
Similarity search - Domain/homology
Probable ribonuclease FAU-1
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsVayssieres, M. / Blaud, M. / Leulliot, N.
Funding support France, 2items
OrganizationGrant numberCountry
Other government
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: RNase W, a conserved ribonuclease family with a novel active site.
Authors: Vayssieres, M. / Juttner, M. / Haas, K. / Ancelin, A. / Marchfelder, A. / Leulliot, N. / Ferreira-Cerca, S. / Blaud, M.
History
DepositionFeb 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ribonuclease FAU-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5613
Polymers48,5131
Non-polymers492
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area19410 Å2
Unit cell
Length a, b, c (Å)76.230, 76.230, 84.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Probable ribonuclease FAU-1 / RNA-binding protein FAU-1


Mass: 48512.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: fau-1, Saci_1213 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4J9H1, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: HEPES pH 7.5, MgCl2, polyacrylic acid (5,100) sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→28.3 Å / Num. obs: 30609 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.54 Å2 / CC1/2: 0.9 / CC star: 0.99 / Net I/σ(I): 8
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3052 / CC1/2: 0.4 / CC star: 0.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
BUSTERrefinement
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→28.3 Å / SU ML: 0.2622 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1531 5 %
Rwork0.1915 29078 -
obs0.1927 30609 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.28 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 2 247 3637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01353454
X-RAY DIFFRACTIONf_angle_d1.24544658
X-RAY DIFFRACTIONf_chiral_restr0.0865514
X-RAY DIFFRACTIONf_plane_restr0.0068596
X-RAY DIFFRACTIONf_dihedral_angle_d15.01951326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.110.31051400.26612650X-RAY DIFFRACTION98.94
2.11-2.180.29171380.24892617X-RAY DIFFRACTION100
2.19-2.270.3241370.28822607X-RAY DIFFRACTION99.71
2.27-2.380.28981400.2372645X-RAY DIFFRACTION99.86
2.38-2.50.28021390.22472641X-RAY DIFFRACTION99.78
2.5-2.660.24171380.22932635X-RAY DIFFRACTION100
2.66-2.860.2481400.21112646X-RAY DIFFRACTION99.93
2.86-3.150.23271390.19632647X-RAY DIFFRACTION99.93
3.15-3.610.17021390.17682652X-RAY DIFFRACTION99.64
3.61-4.540.16561400.15292649X-RAY DIFFRACTION99.22
4.54-28.30.17391410.15552689X-RAY DIFFRACTION99.26

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