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- PDB-5wzj: Structure of APUM23-GGAUUUGACGG -

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Basic information

Entry
Database: PDB / ID: 5wzj
TitleStructure of APUM23-GGAUUUGACGG
Components
  • Pumilio homolog 23
  • RNA (5'-R(*GP*GP*AP*UP*UP*UP*GP*AP*CP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA binding protein / 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: 2.101 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*UP*UP*UP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)69,1892
Polymers69,1892
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-5 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.319, 188.319, 45.383
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*UP*UP*UP*GP*AP*CP*GP*G)-3')


Mass: 3563.162 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.: 166 / 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: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium malonate (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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 54262 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 24.11 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.021 / Rrim(I) all: 0.091 / Χ2: 1.017 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1416.30.5310.9270.1350.5490.996100
2.14-2.1815.30.450.9430.1180.4661.02399.8
2.18-2.22170.4090.9650.1010.4221.038100
2.22-2.26180.3580.9750.0860.3681.051100
2.26-2.3118.10.3110.9820.0740.321.043100
2.31-2.3718.20.2730.9850.0650.2811.034100
2.37-2.4218.20.2430.9890.0580.251.035100
2.42-2.4918.50.2130.9910.0510.2191.028100
2.49-2.5618.50.1870.9940.0440.1921.019100
2.56-2.6518.50.1660.9940.0390.1711.037100
2.65-2.7417.90.1480.9940.0360.1531.049100
2.74-2.8517.10.120.9960.030.1241.047100
2.85-2.9820.20.1080.9980.0240.111.058100
2.98-3.1420.20.0950.9980.0210.0971.039100
3.14-3.3320.30.0790.9990.0180.0811.071100
3.33-3.5920.50.0680.9990.0150.071.059100
3.59-3.9519.20.060.9990.0140.0621.034100
3.95-4.5219.10.0530.9990.0120.0540.962100
4.52-5.720.70.0520.9990.0120.0540.918100
5.7-40180.0470.9990.0110.0490.82199.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WZG

5wzg


Resolution: 2.101→26.115 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.43
RfactorNum. reflection% reflection
Rfree0.1969 2611 4.84 %
Rwork0.1761 --
obs0.1771 53992 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 28.8628 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 2.101→26.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 236 0 166 4546
Biso mean---29.04 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074504
X-RAY DIFFRACTIONf_angle_d0.8296146
X-RAY DIFFRACTIONf_chiral_restr0.046718
X-RAY DIFFRACTIONf_plane_restr0.005744
X-RAY DIFFRACTIONf_dihedral_angle_d15.1272720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1014-2.13960.21551550.187626852840100
2.1396-2.18070.24561170.186727122829100
2.1807-2.22520.25681230.189726962819100
2.2252-2.27360.23651400.186927102850100
2.2736-2.32650.22861120.182126842796100
2.3265-2.38460.22631300.178627252855100
2.3846-2.4490.22681400.190526432783100
2.449-2.5210.23441310.180727532884100
2.521-2.60230.22411500.184826412791100
2.6023-2.69520.22341200.191827562876100
2.6952-2.8030.21911450.196126722817100
2.803-2.93050.22631280.198627122840100
2.9305-3.08470.23251410.19227092850100
3.0847-3.27770.21941670.191926932860100
3.2777-3.53020.20531240.183827292853100
3.5302-3.88440.17241450.164727202865100
3.8844-4.44410.17211520.14932718287099
4.4441-5.590.14521440.15422740288499
5.59-26.11720.14091470.15782683283094
Refinement TLS params.Method: refined / Origin x: 153.6114 Å / Origin y: 136.5498 Å / Origin z: 0.3278 Å
111213212223313233
T0.0882 Å20.0104 Å20.0087 Å2-0.0991 Å2-0.0032 Å2--0.1 Å2
L0.1387 °20.3148 °2-0.0368 °2-0.4692 °2-0.0563 °2--0.1093 °2
S0.0118 Å °0.0131 Å °-0.0141 Å °0.0262 Å °-0.0051 Å °0.0453 Å °0.0402 Å °0.0217 Å °0.0009 Å °
Refinement TLS groupSelection details: all

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