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- PDB-5wzg: Structure of APUM23-GAAUUGACGG -

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Basic information

Entry
Database: PDB / ID: 5wzg
TitleStructure of APUM23-GAAUUGACGG
Components
  • Pumilio homolog 23
  • RNA (5'-R(*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 / Pumilio homolog 23
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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*AP*AP*UP*UP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)68,8672
Polymers68,8672
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint0 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.067, 187.067, 45.269
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*AP*AP*UP*UP*GP*AP*CP*GP*G)-3')


Mass: 3240.997 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.: 35 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
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: BL18U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 30133 / % possible obs: 99.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 37.92 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.038 / Rrim(I) all: 0.126 / Χ2: 0.469 / Net I/σ(I): 3.3 / Num. measured all: 313477
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.599.50.620.8260.2080.6550.45299.9
2.59-2.649.60.5770.8760.1920.6090.45299.8
2.64-2.699.80.5210.8930.1720.550.45599.9
2.69-2.759.90.4560.9170.150.480.451100
2.75-2.819.60.3960.9360.1310.4180.481100
2.81-2.87100.3580.9440.1170.3770.47199.9
2.87-2.94100.3090.9610.1010.3260.486100
2.94-3.029.80.2730.9660.0910.2890.46599.9
3.02-3.119.80.250.9770.0830.2640.482100
3.11-3.219.10.20.9780.0690.2120.48599.9
3.21-3.339.70.1690.9820.0570.1790.53299.7
3.33-3.4610.60.150.990.0480.1570.5399.9
3.46-3.6211.10.1230.9940.0380.1290.53299.8
3.62-3.8111.10.1040.9950.0320.1090.54599.9
3.81-4.0511.50.0970.9960.030.1010.541100
4.05-4.3611.60.0850.9970.0260.0890.51299.9
4.36-4.810.60.0720.9970.0230.0760.47399.9
4.8-5.4911.70.0760.9980.0230.080.43199.9
5.49-6.91120.0750.9980.0220.0790.37999.7
6.91-4010.80.0380.9990.0120.0390.25499.1

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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: SAD / Resolution: 2.55→37.166 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.2169 1458 4.84 %
Rwork0.1812 --
obs0.1829 30109 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.37 Å2 / Biso mean: 39.3293 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 2.55→37.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 215 0 35 4416
Biso mean---36.33 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084477
X-RAY DIFFRACTIONf_angle_d0.9416092
X-RAY DIFFRACTIONf_chiral_restr0.05709
X-RAY DIFFRACTIONf_plane_restr0.005737
X-RAY DIFFRACTIONf_dihedral_angle_d13.9952708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5481-2.63920.28251510.229528382989100
2.6392-2.74480.28421330.224328482981100
2.7448-2.86970.27271360.217228372973100
2.8697-3.02090.2751430.219928613004100
3.0209-3.21010.24871480.212428512999100
3.2101-3.45780.2241530.198328272980100
3.4578-3.80540.19831370.178828622999100
3.8054-4.35530.2051450.157128733018100
4.3553-5.48440.17251580.154728873045100
5.4844-37.17040.18691540.15262967312199

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