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- PDB-4j0x: Structure of Rrp9 -

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Basic information

Entry
Database: PDB / ID: 4j0x
TitleStructure of Rrp9
ComponentsRibosomal RNA-processing protein 9
KeywordsRNA BINDING PROTEIN / Beta-Propeller / WD domain / preribosome
Function / homology
Function and homology information


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) / box C/D methylation guide snoRNP complex / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / 90S preribosome / maturation of SSU-rRNA / small-subunit processome ...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) / box C/D methylation guide snoRNP complex / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / nucleolus / nucleoplasm
Similarity search - Function
Ribosomal RNA-processing protein Rrp9-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily ...Ribosomal RNA-processing protein Rrp9-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ribosomal RNA-processing protein 9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsZhang, L. / Lin, J. / Ye, K.
CitationJournal: Rna / Year: 2013
Title: Structural and functional analysis of the U3 snoRNA binding protein Rrp9.
Authors: Zhang, L. / Lin, J. / Ye, K.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA-processing protein 9
B: Ribosomal RNA-processing protein 9


Theoretical massNumber of molelcules
Total (without water)102,0222
Polymers102,0222
Non-polymers00
Water57632
1
A: Ribosomal RNA-processing protein 9


Theoretical massNumber of molelcules
Total (without water)51,0111
Polymers51,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal RNA-processing protein 9


Theoretical massNumber of molelcules
Total (without water)51,0111
Polymers51,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.445, 78.557, 80.029
Angle α, β, γ (deg.)61.77, 86.44, 71.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ribosomal RNA-processing protein 9


Mass: 51010.793 Da / Num. of mol.: 2 / Fragment: WD DOMAIN, UNP RESIDUES 127-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP9, YPR137W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q06506
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES-K, pH7.5, 25% (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 32300 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 1.7 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.502→19.963 Å / SU ML: 0.32 / σ(F): 1.98 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1642 5.08 %
Rwork0.2176 --
obs0.2199 32299 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5840 0 0 32 5872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045958
X-RAY DIFFRACTIONf_angle_d0.9348026
X-RAY DIFFRACTIONf_dihedral_angle_d16.1962194
X-RAY DIFFRACTIONf_chiral_restr0.068890
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5024-2.57590.38511110.292217580
2.5759-2.65890.32371290.2722248693
2.6589-2.75370.30831390.2472256796
2.7537-2.86360.28851300.2395257596
2.8636-2.99350.31881370.2336262697
2.9935-3.15080.29231310.2374260797
3.1508-3.34730.24871520.2291257297
3.3473-3.60440.27191290.2175261997
3.6044-3.96460.28751370.2129262097
3.9646-4.53240.22681430.1852260997
4.5324-5.68830.21470.1713260298
5.6883-19.96330.23281570.2222259998

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