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- PDB-5wzk: Structure of APUM23-deletion-of-insert-region-GGAAUUGACGG -

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Basic information

Entry
Database: PDB / ID: 5wzk
TitleStructure of APUM23-deletion-of-insert-region-GGAAUUGACGG
Components
  • Pumilio homolog 23
  • RNA (5'-R(*GP*GP*AP*AP*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


response to sucrose / response to glucose / regulation of translation / nucleolus / RNA binding
Similarity search - Function
Nucleolar protein 9 / NOP9-like PUF repeat domain / 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: 2.8 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*AP*UP*UP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)65,2882
Polymers65,2882
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint1 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.060, 189.060, 45.456
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: 61701.574 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 85-235,270-655 / Mutation: deletion
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*AP*UP*UP*GP*AP*CP*GP*G)-3')


Mass: 3586.202 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.: 8 / 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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris (pH 6.5), 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 23439 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 45.51 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.051 / Rrim(I) all: 0.153 / Χ2: 0.429 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.859.20.8380.8350.2920.8880.429100
2.85-2.99.10.7290.8530.2550.7730.44100
2.9-2.969.10.6420.8890.2250.6810.434100
2.96-3.029.10.5890.9070.2060.6240.453100
3.02-3.088.90.5260.9120.1870.5580.44100
3.08-3.158.50.4270.9480.1560.4550.444100
3.15-3.237.90.3440.9460.130.3690.44399.9
3.23-3.328.60.2830.9720.1010.3010.453100
3.32-3.429.70.2480.9810.0840.2620.446100
3.42-3.539.60.210.9850.0710.2220.437100
3.53-3.659.50.1670.9910.0570.1770.442100
3.65-3.89.50.140.9930.0480.1480.448100
3.8-3.979.40.1230.9950.0420.130.441100
3.97-4.189.30.1030.9960.0350.1090.421100
4.18-4.448.90.0840.9970.030.0890.417100
4.44-4.797.80.0720.9970.0270.0780.405100
4.79-5.279.30.0770.9980.0270.0820.4100
5.27-6.039.40.0920.9960.0310.0970.421100
6.03-7.5890.0710.9980.0250.0750.404100
7.58-408.20.0370.9990.0130.0390.369100

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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: 2.8→27.288 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.62
RfactorNum. reflection% reflection
Rfree0.2248 1163 4.97 %
Rwork0.1804 --
obs0.1827 23393 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.75 Å2 / Biso mean: 41.8302 Å2 / Biso min: 13.43 Å2
Refinement stepCycle: final / Resolution: 2.8→27.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 238 0 8 4216
Biso mean---32.44 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084330
X-RAY DIFFRACTIONf_angle_d0.9735915
X-RAY DIFFRACTIONf_chiral_restr0.048692
X-RAY DIFFRACTIONf_plane_restr0.005715
X-RAY DIFFRACTIONf_dihedral_angle_d15.8022611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7992-2.92640.2961310.224827572888
2.9264-3.08050.32341550.232727412896
3.0805-3.27320.26711600.211927392899
3.2732-3.52550.28991450.204827642909
3.5255-3.87940.2141350.172227512886
3.8794-4.43860.20781440.157227772921
4.4386-5.58430.1861470.160428112958
5.5843-27.28970.17491460.164628903036

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