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- PDB-6exx: Crystal Structure of Pes4 RRM4 -

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Basic information

Entry
Database: PDB / ID: 6exx
TitleCrystal Structure of Pes4 RRM4
ComponentsProtein PES4
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif
Function / homology
Function and homology information


mRNA localization resulting in post-transcriptional regulation of gene expression / Deadenylation of mRNA / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...mRNA localization resulting in post-transcriptional regulation of gene expression / Deadenylation of mRNA / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex / nucleus / cytosol
Similarity search - Function
RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsMohamad, N. / Bravo, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF 2015-67077-R Spain
CitationJournal: To Be Published
Title: Crystal Structure of Pes4 RRM4 at 1.1 Angstroms resolution
Authors: Mohamad, N. / Bravo, J.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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

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Assembly

Deposited unit
A: Protein PES4


Theoretical massNumber of molelcules
Total (without water)9,2431
Polymers9,2431
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.501, 36.162, 73.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein PES4 / DNA polymerase epsilon suppressor 4


Mass: 9243.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PES4, YFR023W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39684
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Nitrate 20% PEG 3350 0.1 M Betaine Monohydrate (as an additive)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.1→25.79 Å / Num. obs: 30587 / % possible obs: 99.8 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.05842 / Rrim(I) all: 0.06103 / Net I/σ(I): 21.51
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.6737 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementResolution: 1.1→25.79 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.79
RfactorNum. reflection% reflection
Rfree0.163 1464 4.79 %
Rwork0.1435 --
obs0.1444 30587 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 0 104 756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006695
X-RAY DIFFRACTIONf_angle_d1.001943
X-RAY DIFFRACTIONf_dihedral_angle_d12.834257
X-RAY DIFFRACTIONf_chiral_restr0.059103
X-RAY DIFFRACTIONf_plane_restr0.004122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.13930.21141530.17372860X-RAY DIFFRACTION100
1.1393-1.18490.17071540.15442827X-RAY DIFFRACTION100
1.1849-1.23890.15161200.14522901X-RAY DIFFRACTION100
1.2389-1.30420.18711440.13622871X-RAY DIFFRACTION100
1.3042-1.38590.1521520.12762879X-RAY DIFFRACTION100
1.3859-1.49290.1451280.12372911X-RAY DIFFRACTION100
1.4929-1.64310.12581470.1242913X-RAY DIFFRACTION100
1.6431-1.88080.14271660.13332900X-RAY DIFFRACTION100
1.8808-2.36930.15791460.14682952X-RAY DIFFRACTION100
2.3693-25.79720.18041540.15163109X-RAY DIFFRACTION100

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