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- PDB-2rkj: Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor ... -

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Basic information

Entry
Database: PDB / ID: 2rkj
TitleCocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA
Components
  • RNA (238-MER)
  • RNA (5'-R(P*GP*CP*UP*U)-3')
  • Tyrosyl-tRNA synthetase
KeywordsLigase/RNA / RNA-protein complex / group I intron splicing factor / Aminoacyl-tRNA synthetase / ATP-binding / Ligase / Mitochondrion / mRNA processing / Nucleotide-binding / Protein biosynthesis / Transit peptide / Ligase-RNA COMPLEX
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion ...tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Tyrosyl-tRNA synthetase, C-terminal / Tyrosyl-tRNA synthetase C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Tyrosine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesStaphylococcus phage Twort (virus)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.5 Å
AuthorsPaukstelis, P.J. / Chen, J.-H. / Chase, E. / Lambowitz, A.M. / Golden, B.L.
CitationJournal: Nature / Year: 2008
Title: Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA.
Authors: Paukstelis, P.J. / Chen, J.H. / Chase, E. / Lambowitz, A.M. / Golden, B.L.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (238-MER)
D: RNA (5'-R(P*GP*CP*UP*U)-3')
G: RNA (238-MER)
H: RNA (5'-R(P*GP*CP*UP*U)-3')
K: RNA (238-MER)
L: RNA (5'-R(P*GP*CP*UP*U)-3')
O: RNA (238-MER)
P: RNA (5'-R(P*GP*CP*UP*U)-3')
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
E: Tyrosyl-tRNA synthetase
F: Tyrosyl-tRNA synthetase
I: Tyrosyl-tRNA synthetase
J: Tyrosyl-tRNA synthetase
M: Tyrosyl-tRNA synthetase
N: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)682,20516
Polymers682,20516
Non-polymers00
Water0
1
C: RNA (238-MER)
D: RNA (5'-R(P*GP*CP*UP*U)-3')
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)170,5514
Polymers170,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
MethodPISA
2
G: RNA (238-MER)
H: RNA (5'-R(P*GP*CP*UP*U)-3')
E: Tyrosyl-tRNA synthetase
F: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)170,5514
Polymers170,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
MethodPISA
3
K: RNA (238-MER)
L: RNA (5'-R(P*GP*CP*UP*U)-3')
I: Tyrosyl-tRNA synthetase
J: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)170,5514
Polymers170,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
MethodPISA
4
O: RNA (238-MER)
P: RNA (5'-R(P*GP*CP*UP*U)-3')
M: Tyrosyl-tRNA synthetase
N: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)170,5514
Polymers170,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.063, 123.525, 235.231
Angle α, β, γ (deg.)90.000, 90.260, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: RNA chain
RNA (238-MER)


Mass: 79489.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage Twort (virus) / Genus: SPO1-like viruses / Gene: orf142-I2 / Genus (production host): SPO1-like viruses / Production host: Staphylococcus phage Twort (virus)
#2: RNA chain
RNA (5'-R(P*GP*CP*UP*U)-3')


Mass: 1217.762 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
Tyrosyl-tRNA synthetase / Tyrosine-tRNA ligase / TyrRS


Mass: 44922.129 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: cyt-18 / Production host: Escherichia coli (E. coli) / References: UniProt: P12063, tyrosine-tRNA ligase

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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: 4.92 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M cacodylate, 1.8 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylateCacodylic acid11
2ammonium sulfate11
3cacodylateCacodylic acid12
4ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2006
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. all: 79214 / Num. obs: 66194 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Χ2: 1.389 / Net I/σ(I): 11
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.86 / Num. unique all: 3375 / Χ2: 1.037 / % possible all: 42.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1Y42, 1Y0Q

1y42

1y0q


Resolution: 4.5→47.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 7898242.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3330 5 %RANDOM
Rwork0.235 ---
all-79214 --
obs-66048 83.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 202.284 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 211.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.54 Å20 Å2-0.31 Å2
2--12.64 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.66 Å
Luzzati d res low-50 Å
Luzzati sigma a0.71 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 4.5→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23616 20720 0 0 44336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.632
X-RAY DIFFRACTIONc_scbond_it1.181.5
X-RAY DIFFRACTIONc_scangle_it1.972
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 327 5 %
Rwork0.355 6167 -
all-6494 -
obs--49.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3dna-rna.param

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