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- PDB-1vs3: Crystal Structure of the tRNA Pseudouridine Synthase TruA From Th... -

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Basic information

Entry
Database: PDB / ID: 1vs3
TitleCrystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8
ComponentstRNA pseudouridine synthase A
KeywordsISOMERASE / TruA / pseudouridine synthase / tRNA modification / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNA pseudouridine38-40 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / RNA binding
Similarity search - Function
Pseudouridine synthase I, catalytic domain, C-terminal subdomain / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsDong, X. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Rna Biol. / Year: 2006
Title: Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.
Authors: Dong, X. / Bessho, Y. / Shibata, R. / Nishimoto, M. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJun 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Dec 27, 2023Group: 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 A
B: tRNA pseudouridine synthase A


Theoretical massNumber of molelcules
Total (without water)55,5072
Polymers55,5072
Non-polymers00
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-3 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.530, 91.530, 163.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

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


Mass: 27753.268 Da / Num. of mol.: 2 / Fragment: residues 1-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: truA / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q5SHU9, tRNA pseudouridine38-40 synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 6% PEG2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONPhoton Factory AR-NW12A10.97924, 0.97954, 0.9700
SYNCHROTRONSPring-8 BL26B1211
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 12, 2005
ADSC QUANTUM 2102CCDJul 30, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double flat Si (III) crystalsMADMx-ray1
2double flat Si (III) crystalsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979541
30.971
411
ReflectionResolution: 2.25→50 Å / Num. obs: 33977 / % possible obs: 100 % / Redundancy: 15.1 % / Biso Wilson estimate: 28.8 Å2
Reflection shellResolution: 2.25→2.33 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→44.08 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2374361.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1692 5 %RANDOM
Rwork0.222 ---
obs0.222 33855 100 %-
all-33975 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.7827 Å2 / ksol: 0.34011 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2--2.37 Å20 Å2
3----4.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.25→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 565 4477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 185 4.4 %
Rwork0.264 3975 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water.param

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