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- PDB-7yw2: Crystal structure of tRNA 2'-phosphotransferase from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 7yw2
TitleCrystal structure of tRNA 2'-phosphotransferase from Mus musculus
ComponentstRNA 2'-phosphotransferase 1
KeywordsTRANSFERASE / tRNA 2'-phosphotransferase
Function / homology
Function and homology information


2'-phosphotransferase / tRNA 2'-phosphotransferase activity / tRNA splicing, via endonucleolytic cleavage and ligation
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
GLYCINE / Chem-HQG / PHOSPHATE ION / sorbitol / tRNA 2'-phosphotransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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

Downloads & links

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Assembly

Deposited unit
A: tRNA 2'-phosphotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,84820
Polymers27,3931
Non-polymers2,45619
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.585, 65.585, 148.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein tRNA 2'-phosphotransferase 1 / mTPT1


Mass: 27392.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpt1, Tpt1h / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3A2, 2'-phosphotransferase
#7: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 6 types, 93 molecules

#2: Chemical ChemComp-HQG / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.36 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 16% PEG 8000 40 mM Potassium phosphate dibasic 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.23→74.23 Å / Num. obs: 34775 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 49.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.019 / Rrim(I) all: 0.054 / Net I/σ(I): 22.2
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
2.23-2.38.10.5671366216930.9380.210.6063.399.6
8.92-74.236.70.02724423620.9990.0110.02952.499.7

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6e3a

6e3a


Resolution: 2.23→56.8 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1599 4.6 %
Rwork0.2016 33176 -
obs0.2026 34775 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.71 Å2 / Biso mean: 60.1087 Å2 / Biso min: 42.87 Å2
Refinement stepCycle: final / Resolution: 2.23→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 158 76 1819
Biso mean--56.22 57.28 -
Num. residues----206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.23-2.30.31281450.295130183163
2.3-2.380.29591480.292230113159
2.38-2.480.33241580.270729913149
2.48-2.590.26641600.248630253185
2.59-2.730.29611540.282529953149
2.73-2.90.28731030.25930623165
2.9-3.120.28731340.248630443178
3.12-3.440.29621380.208530223160
3.44-3.940.24241600.199729823142
3.94-4.960.15611290.148430413170
4.96-56.80.15611700.164229853155
Refinement TLS params.Method: refined / Origin x: -32.1607 Å / Origin y: -0.6389 Å / Origin z: 22.9931 Å
111213212223313233
T0.6741 Å20.2051 Å20.0249 Å2-0.3468 Å20.0169 Å2--0.4879 Å2
L1.2718 °2-0.7187 °2-0.6485 °2-2.1299 °21.0943 °2--3.8394 °2
S0.2985 Å °0.3445 Å °0.0799 Å °-0.3876 Å °-0.3376 Å °0.0774 Å °-0.7375 Å °-0.3523 Å °0.0373 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 224
2X-RAY DIFFRACTION1allA300 - 318
3X-RAY DIFFRACTION1allS1 - 93

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