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- PDB-7yw3: Crystal structure of tRNA 2'-phosphotransferase from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 7yw3
TitleCrystal structure of tRNA 2'-phosphotransferase from Homo sapiens
ComponentstRNA 2'-phosphotransferase 1
KeywordsTRANSFERASE / tRNA 2'-phosphotransferase
Function / homology2'-phosphotransferase / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family / tRNA 2'-phosphotransferase activity / tRNA splicing, via endonucleolytic cleavage and ligation / Chem-HQG / tRNA 2'-phosphotransferase 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4833
Polymers27,7821
Non-polymers7012
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint4 kcal/mol
Surface area10610 Å2
Unit cell
Length a, b, c (Å)53.908, 84.062, 101.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein tRNA 2'-phosphotransferase 1


Mass: 27781.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86TN4, 2'-phosphotransferase
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1M Tris pH 8.0 28 % PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→25.38 Å / Num. obs: 8284 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Net I/σ(I): 11.8 / Num. measured all: 53150
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
2.5-2.66.70.65961649170.9540.2740.7143.3100
9.01-25.3850.0489731960.9980.0240.05430.394.5

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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: 2.5→25.38 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2949 413 5.02 %
Rwork0.252 7814 -
obs0.2542 8227 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.02 Å2 / Biso mean: 48.2627 Å2 / Biso min: 27.32 Å2
Refinement stepCycle: final / Resolution: 2.5→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 42 8 1611
Biso mean--43.96 51.33 -
Num. residues----205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.860.38161320.317325562688
2.86-3.60.33761390.271925762715
3.6-25.380.24941420.22326822824

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