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- PDB-1r3f: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA... -

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Basic information

Entry
Database: PDB / ID: 1r3f
TitleCrystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
ComponentstRNA pseudouridine synthase B
KeywordsLYASE / RNA modification / pseudouridylation
Function / homology
Function and homology information


tRNA folding / tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / tRNA binding / cytosol
Similarity search - Function
tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal / Pseudouridine synthase II TruB, C-terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain ...tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal / Pseudouridine synthase II TruB, C-terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsPan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit
Authors: Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M.
History
DepositionOct 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)35,1321
Polymers35,1321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.03, 71.01, 48.67
Angle α, β, γ (deg.)90, 117.87, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase / P35 protein


Mass: 35132.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TRUB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P60340, pseudouridylate synthase

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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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4K, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
210 mMTris1droppH7.5
32 mMEDTA1drop
42 mMdithiothreitol1drop
58-10 %(w/v)PEG40001reservoir
60.2 mMmagnesium sulfate1reservoir
7100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97926, 0.97942, 0.9610
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2001 / Details: mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979421
30.9611
ReflectionResolution: 1.85→40 Å / Num. all: 24806 / Num. obs: 24806 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.97 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 23.7
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.47 / % possible all: 100
Reflection
*PLUS
Num. measured all: 426647
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.47

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→50 Å / σ(F): 1.85 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 2425 RANDOM
Rwork0.228 --
obs0.228 48520 -
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 0 0 2158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.006
X-RAY DIFFRACTIONc_angle_deg1.29
LS refinement shellResolution: 1.85→1.96 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.228
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 46517
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d

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