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- PDB-5wzh: Structure of APUM23-GGAAUUGACGG -

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Basic information

Entry
Database: PDB / ID: 5wzh
TitleStructure of APUM23-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: 2.509 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)69,2122
Polymers69,2122
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-0 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.409, 188.409, 45.720
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*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.: 24 / 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: 3.38 Å3/Da / Density % sol: 63.66 %
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: 2.5→40 Å / Num. obs: 31090 / % possible obs: 96.5 % / Redundancy: 12.6 % / Biso Wilson estimate: 44.26 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.121 / Χ2: 1.486 / Net I/σ(I): 7.1 / Num. measured all: 392238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5412.80.7630.7540.2270.7981.00897.3
2.54-2.5912.70.6350.8280.1880.6651.046100
2.59-2.6412.90.6060.8670.1770.6331.06396.2
2.64-2.6912.70.5490.8620.1640.5751.12896.6
2.69-2.7512.70.4360.9150.1280.4561.09899.9
2.75-2.82130.3780.9380.1090.3941.15794.7
2.82-2.8912.90.3250.9450.0950.341.15898.3
2.89-2.9612.70.2760.9630.080.2881.20197.6
2.96-3.0512.90.2420.9750.070.2531.29595.5
3.05-3.1512.70.2060.9810.060.2151.29199.1
3.15-3.26130.1640.990.0470.1711.41294.4
3.26-3.3912.70.1370.9920.0390.1421.54998.5
3.39-3.5512.70.1310.9930.0370.1361.81395.3
3.55-3.7312.40.1130.9960.0320.1182.11596.1
3.73-3.9711.90.0990.9960.0290.1032.26597.7
3.97-4.27120.0880.9970.0260.0922.32695.3
4.27-4.711.80.0850.9970.0250.0892.61295.3
4.7-5.3812.40.0760.9970.0210.0791.97795.6
5.38-6.7812.80.0580.9990.0160.061.23493.9
6.78-4012.50.0420.9980.0120.0441.23994

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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: 2.509→39.884 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.229 1495 4.81 %
Rwork0.1871 --
obs0.1891 31069 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.14 Å2 / Biso mean: 43.5345 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 2.509→39.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 238 0 24 4376
Biso mean---39.8 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074476
X-RAY DIFFRACTIONf_angle_d0.9116114
X-RAY DIFFRACTIONf_chiral_restr0.046717
X-RAY DIFFRACTIONf_plane_restr0.005740
X-RAY DIFFRACTIONf_dihedral_angle_d14.5832694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5094-2.59040.34871310.2732578270994
2.5904-2.68290.31821570.24142666282396
2.6829-2.79030.23591530.22052694284799
2.7903-2.91730.26361060.20682723282997
2.9173-3.0710.3041420.21422659280196
3.071-3.26330.26611330.21622698283196
3.2633-3.51520.22431300.19512704283497
3.5152-3.86860.2231300.17642709283997
3.8686-4.42780.19761170.16552702281996
4.4278-5.57620.19641510.16912680283195
5.5762-39.88910.19511450.16172761290694

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