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- PDB-7yw4: Crystal structure of tRNA 2'-phosphotransferase from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 7yw4
TitleCrystal structure of tRNA 2'-phosphotransferase from Saccharomyces cerevisiae
ComponentstRNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-phosphotransferase
Function / homology
Function and homology information


2'-phosphotransferase / tRNA 2'-phosphotransferase activity / tRNA splicing, via endonucleolytic cleavage and ligation / nucleus / cytoplasm
Similarity search - Function
Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D(-)-TARTARIC ACID / tRNA 2'-phosphotransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation.
Authors: Yang, X. / Wang, J. / Li, S. / Li, X. / Gong, J. / Yan, Z. / Zhou, H. / Wu, C. / Liu, X.
History
DepositionAug 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0543
Polymers26,2401
Non-polymers8142
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-3 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.672, 41.672, 129.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein tRNA 2'-phosphotransferase


Mass: 26240.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TPT1, YOL102C, HRE230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12272, 2'-phosphotransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.23 Å3/Da / Density % sol: 25 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1.4 M Ammonium tartrate dibasic 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.18→36.09 Å / Num. obs: 7305 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 43.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.031 / Rrim(I) all: 0.1 / Net I/σ(I): 13.4 / Num. measured all: 77298
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.2510.50.54663486060.960.1750.5743.9100
9-36.0980.05411141400.9980.0190.05725.399.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6e3a

6e3a


Resolution: 2.18→36.09 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 332 4.58 %
Rwork0.2371 6923 -
obs0.2382 7255 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.13 Å2 / Biso mean: 57.6322 Å2 / Biso min: 33.89 Å2
Refinement stepCycle: final / Resolution: 2.18→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 49 16 999
Biso mean--65.07 52.92 -
Num. residues----120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.18-2.750.35681520.334733793531
2.75-36.090.24211800.21335443724

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