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- PDB-7r9g: Catalytically inactive yeast Pseudouridine Synthase, PUS1, bound ... -

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Basic information

Entry
Database: PDB / ID: 7r9g
TitleCatalytically inactive yeast Pseudouridine Synthase, PUS1, bound to RNA
Components
  • RNA (5'-R(*AP*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 / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / tRNA pseudouridine synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthesis / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / mRNA processing / mRNA binding ...snRNA pseudouridine synthase activity / tRNA pseudouridine synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthesis / snRNA 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: 2.4 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(*AP*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)68,1264
Polymers67,9942
Non-polymers1322
Water90150
1
A: tRNA pseudouridine synthase 1
B: RNA (5'-R(*AP*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(*AP*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)136,2518
Polymers135,9884
Non-polymers2634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5630 Å2
ΔGint-89 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.195, 98.344, 72.239
Angle α, β, γ (deg.)90.000, 102.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-747-

HOH

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Components

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


Mass: 62197.551 Da / Num. of mol.: 1 / Mutation: D134A
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(*AP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3')


Mass: 5796.515 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Ammonium sulfate, 0.05 M Bis-Tris pH 6.0, 26% Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27638 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Χ2: 0.74 / Net I/σ(I): 8 / Num. measured all: 178541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.445.30.63213000.8130.2910.6980.45795.1
2.44-2.495.50.55913530.840.2540.6160.4497.4
2.49-2.536.10.52413480.8990.2260.5720.44298.9
2.53-2.596.30.44713910.9140.1910.4870.46499.7
2.59-2.646.20.39213770.9420.1710.4280.46899.9
2.64-2.76.80.33913590.9650.1390.3670.461100
2.7-2.776.90.31514070.970.1280.340.488100
2.77-2.856.70.28213700.970.1160.3060.49100
2.85-2.936.60.21313830.9830.090.2320.522100
2.93-3.026.30.17913860.9840.0770.1950.59100
3.02-3.136.70.14913980.990.0620.1610.658100
3.13-3.266.50.11313880.9930.0480.1230.752100
3.26-3.416.80.09413990.9950.0380.1020.897100
3.41-3.586.90.0813790.9970.0330.0861.021100
3.58-3.816.60.06713850.9970.0280.0730.921100
3.81-4.16.50.05913790.9980.0250.0651.011100
4.1-4.526.50.05714050.9970.0240.0621.12199.9
4.52-5.176.80.05314110.9980.0220.0571.098100
5.17-6.516.40.04913990.9980.0210.0541.08100
6.51-506.50.04114210.9980.0170.0441.193100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å49.17 Å
Translation2.4 Å49.17 Å

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J37

4j37


Resolution: 2.4→49.17 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1993 7.21 %
Rwork0.2216 25640 -
obs0.2247 27633 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.19 Å2 / Biso mean: 65.2741 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.4→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 254 6 50 3229
Biso mean--62.74 58.11 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023277
X-RAY DIFFRACTIONf_angle_d0.5094493
X-RAY DIFFRACTIONf_dihedral_angle_d6.245552
X-RAY DIFFRACTIONf_chiral_restr0.039500
X-RAY DIFFRACTIONf_plane_restr0.002537
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.32771270.28921732185995
2.46-2.530.37261430.27421809195298
2.53-2.60.29021400.255418281968100
2.6-2.690.30881450.253118181963100
2.69-2.780.26861420.248318281970100
2.78-2.890.32541460.262718722018100
2.89-3.030.28691400.25217891929100
3.03-3.190.32261440.270318371981100
3.19-3.380.30541340.247118411975100
3.38-3.650.2521480.232918642012100
3.65-4.010.2741470.204518411988100
4.01-4.590.21221410.187818311972100
4.59-5.790.22841510.19818652016100
5.79-49.170.2511450.205118852030100

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