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- PDB-5wzi: Structure of APUM23-GGAGUUGACGG -

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Basic information

Entry
Database: PDB / ID: 5wzi
TitleStructure of APUM23-GGAGUUGACGG
Components
  • Pumilio homolog 23
  • RNA (5'-R(*GP*GP*AP*GP*UP*UP*GP*AP*CP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / SIGNALING PROTEIN / HYDROLASE / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to sucrose / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / ribosomal small subunit export from nucleus / response to glucose / 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 / regulation of translation / nucleolus / RNA binding
Similarity search - Function
Nucleolar protein 9 / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Pumilio homolog 23
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBao, H. / Wang, N. / Wang, C. / Jiang, Y. / Wu, J. / Shi, Y.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis for the specific recognition of 18S rRNA by APUM23.
Authors: Bao, H. / Wang, N. / Wang, C. / Jiang, Y. / Liu, J. / Xu, L. / Wu, J. / Shi, Y.
History
DepositionJan 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pumilio homolog 23
B: RNA (5'-R(*GP*GP*AP*GP*UP*UP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)69,2282
Polymers69,2282
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-6 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.497, 190.497, 45.727
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pumilio homolog 23 / AtPUM23


Mass: 65626.008 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 85-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: APUM23, At1g72320, T10D10.21, T9N14.7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9C552
#2: RNA chain RNA (5'-R(*GP*GP*AP*GP*UP*UP*GP*AP*CP*GP*G)-3')


Mass: 3602.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-Malic acid (pH 7.0), 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 25175 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.043 / Rrim(I) all: 0.15 / Χ2: 0.954 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.811.80.7770.9140.2340.8120.944100
2.8-2.8511.70.6690.9230.2020.70.948100
2.85-2.911.90.5550.9430.1660.580.9399.9
2.9-2.9611.90.4740.9580.1420.4950.945100
2.96-3.0311.80.4430.9640.1330.4630.949100
3.03-3.1120.380.970.1130.3960.942100
3.1-3.1711.90.3280.9810.0980.3430.967100
3.17-3.26120.250.9850.0750.2610.911100
3.26-3.3612.10.2120.9910.0630.2220.918100
3.36-3.46120.1920.9910.0570.20.946100
3.46-3.5912.10.1840.9930.0540.1920.94999.9
3.59-3.7311.50.1480.9920.0450.1551.188100
3.73-3.912.20.1320.9940.0390.1370.98100
3.9-4.1112.30.1150.9970.0340.120.976100
4.11-4.3612.10.10.9960.030.1051.03100
4.36-4.711.80.0910.9960.0280.0951.077100
4.7-5.1711.70.0910.9960.0280.0961.024100
5.17-5.9211.80.0940.9960.0280.0980.916100
5.92-7.4511.80.0740.9970.0220.0770.721100
7.45-4011.30.0670.9970.020.070.83999.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WZG

5wzg


Resolution: 2.75→39.993 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.05
RfactorNum. reflection% reflection
Rfree0.2419 1277 5.09 %
Rwork0.1887 --
obs0.1914 25105 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.26 Å2 / Biso mean: 40.2085 Å2 / Biso min: 13.9 Å2
Refinement stepCycle: final / Resolution: 2.75→39.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 239 0 22 4361
Biso mean---35.73 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084437
X-RAY DIFFRACTIONf_angle_d0.9326054
X-RAY DIFFRACTIONf_chiral_restr0.048713
X-RAY DIFFRACTIONf_plane_restr0.006726
X-RAY DIFFRACTIONf_dihedral_angle_d14.5162665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7503-2.86040.28461370.22592620275799
2.8604-2.99050.28261340.212425762710100
2.9905-3.14810.27911340.217826492783100
3.1481-3.34530.27861550.207826262781100
3.3453-3.60340.2681460.199526162762100
3.6034-3.96580.251350.19572640277599
3.9658-4.53890.24461110.16512697280899
4.5389-5.71590.21431610.175326632824100
5.7159-39.99730.20011640.170527412905100

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