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- PDB-1si7: Structure of E. coli tRNA psi 13 pseudouridine synthase TruD -

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Basic information

Entry
Database: PDB / ID: 1si7
TitleStructure of E. coli tRNA psi 13 pseudouridine synthase TruD
ComponentstRNA pseudouridine synthase D
KeywordsLYASE / TruD / pseudouridine synthase / tRNA / novel fold
Function / homology
Function and homology information


tRNA pseudouridine13 synthase / pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
Pseudouridine synthase / TruD, insertion domain / Pseudouridine synthase, TruD, insertion domain superfamily / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD, catalytic domain ...Pseudouridine synthase / TruD, insertion domain / Pseudouridine synthase, TruD, insertion domain superfamily / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD, catalytic domain / Pseudouridine synthase, TruD / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaya, Y. / Del Campo, M. / Ofengand, J. / Malhotra, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold
Authors: Kaya, Y. / Del Campo, M. / Ofengand, J. / Malhotra, A.
History
DepositionFeb 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)41,3121
Polymers41,3121
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.479, 63.479, 112.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein tRNA pseudouridine synthase D / Pseudouridylate synthase / Uracil hydrolyase


Mass: 41311.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TRUD / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57261, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.7 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, PEG 8000, ethylene glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
220 mMHEPES1droppH8.0
3250 mM1dropNaCl
42 mMEDTA1drop
52 mMdithiothreitol1drop
625 %(v/v)ethylene gylcol1drop
70.1 MMES1reservoirpH6.0
812-14 %(w/v)PEG80001reservoir
925 %(v/v)ethylene glycol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.97904
SYNCHROTRONNSLS X12C20.97865
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 15, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.978651
ReflectionResolution: 2.2→40 Å / Num. all: 22547 / Num. obs: 22262 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 30.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.1 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 88054
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished TruD model SAD data on selenomethionine labeled protein

Resolution: 2.2→35.05 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 635612.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1051 4.8 %RANDOM
Rwork0.212 ---
obs0.212 21744 96.5 %-
all-21744 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9673 Å2 / ksol: 0.333292 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2--2.22 Å20 Å2
3----5.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 240 2912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 177 5.2 %
Rwork0.255 3205 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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