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- PDB-7tuv: Crystal structure of the exoribonucleolytic module of T. brucei RRP44 -

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Basic information

Entry
Database: PDB / ID: 7tuv
TitleCrystal structure of the exoribonucleolytic module of T. brucei RRP44
Components
  • RNA (5'-R(P*GP*GP*UP*U)-3')
  • Ribonuclease RRP44
KeywordsHYDROLASE/RNA / ribonuclease / RNaseII family / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


exosome (RNase complex) / RNA nuclease activity / RNA binding / nucleus / metal ion binding
Similarity search - Function
PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain ...PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / PIN domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / RNA / Rrp44p homologue
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.225 Å
AuthorsCesaro, G. / Guimaraes, B.G.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)442323/2019-0 Brazil
Other governmentInova-3501948026 Brazil
Other governmentCAPES-COFECUB 862/2015 Brazil
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates.
Authors: Cesaro, G. / da Soler, H.T. / Guerra-Slompo, E.P. / Haouz, A. / Legrand, P. / Zanchin, N.I.T. / Guimaraes, B.G.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease RRP44
B: RNA (5'-R(P*GP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9905
Polymers85,6172
Non-polymers3733
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-38 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.296, 91.113, 148.305
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease RRP44


Mass: 84359.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: RRP44 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95Z12
#2: RNA chain RNA (5'-R(P*GP*GP*UP*U)-3')


Mass: 1257.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 15% (w/v) PEG 20000, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.225→77.632 Å / Num. obs: 24678 / % possible obs: 93.8 % / Redundancy: 24 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 2.225→2.554 Å / Num. unique obs: 1235 / CC1/2: 0.632 / % possible all: 70.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.225→77.63 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.865 / SU R Cruickshank DPI: 0.91 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.264 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.344
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 1292 -RANDOM
Rwork0.1941 ---
obs0.1977 24678 55 %-
Displacement parametersBiso mean: 49.61 Å2
Baniso -1Baniso -2Baniso -3
1-5.2273 Å20 Å20 Å2
2---9.5586 Å20 Å2
3---4.3312 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.225→77.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 110 253 5694
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095554HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.967540HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1934SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes951HARMONIC5
X-RAY DIFFRACTIONt_it5554HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion718SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4407SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion18.7
LS refinement shellResolution: 2.23→2.43 Å
RfactorNum. reflection% reflection
Rfree0.3757 23 -
Rwork0.2712 --
obs0.2762 494 4.9 %
Refinement TLS params.Origin x: 29.5012 Å / Origin y: -9.2357 Å / Origin z: 21.9302 Å
111213212223313233
T0.0146 Å2-0.0587 Å20.0344 Å2--0.2148 Å2-0.0314 Å2---0.0609 Å2
L0.8346 °2-0.2702 °20.2362 °2-1.0256 °2-0.1465 °2--0.7124 °2
S-0.084 Å °-0.1232 Å °0.0212 Å °-0.1232 Å °0.0091 Å °-0.0158 Å °0.0212 Å °-0.0158 Å °0.0749 Å °
Refinement TLS groupSelection details: { A|* }

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