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- PDB-7r9f: Wild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorour... -

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Basic information

Entry
Database: PDB / ID: 7r9f
TitleWild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorouracil RNA
Components
  • RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')
  • tRNA pseudouridine synthase 1
KeywordsRNA BINDING PROTEIN/RNA / pseudouridine / pus / pus1 / rna / synthase / mRNA / yeast / pseudo uracil / pseudouracil / uracil / saccharomyces cerevisiae / inactive / catalytically inactive / dead / pseudouridine synthase / RNA BINDING PROTEIN / 5-Fluorouracil / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / mRNA processing / mRNA binding / nucleoplasm / nucleus
Similarity search - Function
Pseudouridine synthase PUS1/ PUS2-like / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA pseudouridine synthase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsDoyle, L.A. / Stoddard, B.L.
CitationJournal: Plos One / Year: 2023
Title: The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.
Authors: Grunberg, S. / Doyle, L.A. / Wolf, E.J. / Dai, N. / Correa Jr., I.R. / Yigit, E. / Stoddard, B.L.
History
DepositionJun 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA pseudouridine synthase 1
B: RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0493
Polymers67,9532
Non-polymers961
Water00
1
A: tRNA pseudouridine synthase 1
B: RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')
hetero molecules

A: tRNA pseudouridine synthase 1
B: RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0986
Polymers135,9064
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6320 Å2
ΔGint-65 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.466, 134.466, 158.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein tRNA pseudouridine synthase 1 / tRNA pseudouridylate synthase 1 / tRNA-uridine isomerase 1


Mass: 62241.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUS1, YPL212C / Production host: Escherichia coli (E. coli)
References: UniProt: Q12211, Isomerases; Intramolecular transferases; Transferring other groups
#2: RNA chain RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')


Mass: 5711.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium sodium tartrate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00915 Å / Relative weight: 1
ReflectionResolution: 2.89→48.02 Å / Num. obs: 19540 / % possible obs: 100 % / Redundancy: 38.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.041 / Rrim(I) all: 0.256 / Net I/σ(I): 14.6 / Num. measured all: 746212 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.89-3.0740.14.91212393230940.4650.7774.9741.2100
8.67-48.02300.064251618400.9990.0110.06554.599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å46.88 Å
Translation2.89 Å46.88 Å

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J37

4j37


Resolution: 2.89→46.88 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 1950 10.01 %
Rwork0.2512 17540 -
obs0.2551 19490 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.22 Å2 / Biso mean: 90.8162 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.89→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 273 5 0 2973
Biso mean--109.72 --
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033069
X-RAY DIFFRACTIONf_angle_d0.5334235
X-RAY DIFFRACTIONf_dihedral_angle_d17.115546
X-RAY DIFFRACTIONf_chiral_restr0.038481
X-RAY DIFFRACTIONf_plane_restr0.003506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.89-2.960.41781360.40612221358
2.96-3.040.42521360.363412181354
3.04-3.130.38281360.32312321368
3.13-3.230.39171360.304312221358
3.23-3.350.3411380.291912371375
3.35-3.480.34761340.30112151349
3.48-3.640.31021400.282212521392
3.64-3.830.33241370.26812321369
3.83-4.070.28171380.245312491387
4.07-4.390.28171380.233312361374
4.39-4.830.23121400.199912681408
4.83-5.530.29081410.235512661407
5.53-6.950.2741450.261612981443
6.96-46.880.25631550.226913931548

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