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- PDB-5nlg: RRP5 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5nlg
TitleRRP5 C-terminal domain
ComponentsrRNA biogenesis protein RRP5
KeywordsNUCLEAR PROTEIN / Ribosome biogenesis 90S TPR domain
Function / homology
Function and homology information


box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / 90S preribosome assembly / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding ...box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / 90S preribosome assembly / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / mRNA binding / nucleolus / RNA binding / nucleoplasm
Similarity search - Function
: / : / rRNA biogenesis protein Rrp5 / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
rRNA biogenesis protein RRP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsThore, S. / Fribourg, S.
CitationJournal: FEBS Open Bio / Year: 2018
Title: Structural and interaction analysis of the Rrp5 C-terminal region.
Authors: Perebaskine, N. / Thore, S. / Fribourg, S.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rRNA biogenesis protein RRP5


Theoretical massNumber of molelcules
Total (without water)36,7011
Polymers36,7011
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.010, 114.010, 65.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1851-

HOH

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Components

#1: Protein rRNA biogenesis protein RRP5 / Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA- ...Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA-associated protein RRP5


Mass: 36701.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP5, FMI1, YMR229C, YM9959.11C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05022
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 16-21% PEG1000 100mM Sodium/potassium phosphate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.35→39.476 Å / Num. obs: 20756 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.133 % / Biso Wilson estimate: 40.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.104 / Χ2: 0.966 / Net I/σ(I): 13.17 / Num. measured all: 106545 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.414.4460.9731.726629151214910.6641.10298.6
2.41-2.484.9550.7292.487314147814760.7740.81699.9
2.48-2.555.4330.633.167736142414240.8090.699100
2.55-2.635.3940.513.87605141014100.880.565100
2.63-2.715.3490.4334.477264135913580.9010.4899.9
2.71-2.815.3540.355.647072132313210.9280.38999.8
2.81-2.915.3250.2587.236720126212620.9630.286100
2.91-3.035.3230.2058.916499122112210.9770.228100
3.03-3.175.2970.1610.976282118711860.9820.17799.9
3.17-3.325.2650.11114.325891112011190.9910.12499.9
3.32-3.55.1930.08917.055634108610850.9940.09999.9
3.5-3.725.0970.06820.285189101910180.9960.07699.9
3.72-3.974.9470.05823.147109529520.9970.064100
3.97-4.294.6610.05224.4541448978890.9960.05899.1
4.29-4.74.2950.04524.3736518548500.9970.05199.5
4.7-5.265.1990.04428.9438067337320.9980.04999.9
5.26-6.075.4990.03930.6436846706700.9990.043100
6.07-7.435.4250.0431.6631305775770.9990.045100
7.43-10.515.2510.02742.12234244644610.03100
10.51-39.4764.6210.02545.9412432752690.9990.02997.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.476 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2002 9.65 %
Rwork0.1978 18749 -
obs0.2019 20751 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.02 Å2 / Biso mean: 52.0095 Å2 / Biso min: 22.46 Å2
Refinement stepCycle: final / Resolution: 2.35→39.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 0 151 2420
Biso mean---46.07 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092313
X-RAY DIFFRACTIONf_angle_d0.893111
X-RAY DIFFRACTIONf_chiral_restr0.052336
X-RAY DIFFRACTIONf_plane_restr0.005397
X-RAY DIFFRACTIONf_dihedral_angle_d20.6291400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.40890.36231350.31991267140298
2.4089-2.4740.34111400.282813501490100
2.474-2.54680.31611410.266313201461100
2.5468-2.6290.32461410.248213281469100
2.629-2.72290.26321440.23813281472100
2.7229-2.83190.28311410.23413211462100
2.8319-2.96070.2721460.231813311477100
2.9607-3.11680.27721380.229513451483100
3.1168-3.31190.30631450.214313331478100
3.3119-3.56750.24681440.194213481492100
3.5675-3.92620.21951480.165413471495100
3.9262-4.49370.18881440.15951340148499
4.4937-5.65890.21451420.163213641506100
5.6589-39.48170.18021530.174214271580100

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