[English] 日本語
Yorodumi
- PDB-6ede: tRNA 2'-phosphotransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ede
TitletRNA 2'-phosphotransferase
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / KptA / Tpt1 / TRPT1
Function / homology
Function and homology information


tRNA 2'-phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+ poly-ADP-ribosyltransferase activity
Similarity search - Function
RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain / RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HQG / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å
AuthorsShuman, S. / Goldgur, Y. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM126945 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.
Authors: Banerjee, A. / Munir, A. / Abdullahu, L. / Damha, M.J. / Goldgur, Y. / Shuman, S.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0752
Polymers23,4361
Non-polymers6391
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.284, 53.284, 308.393
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1192-

HOH

-
Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 23435.961 Da / Num. of mol.: 1 / Mutation: C46S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: kptA, Cthe_3059
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A3DJX6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.0, 10 %MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 39099 / % possible obs: 99.3 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rpim(I) all: 0.014 / Net I/σ(I): 56.6
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 2.8 / CC1/2: 0.884 / Rpim(I) all: 0.208 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E3A

6e3a


Resolution: 1.553→46.145 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1876 2000 5.14 %
Rwork0.1727 --
obs0.1735 38941 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.553→46.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 40 201 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051537
X-RAY DIFFRACTIONf_angle_d0.8532082
X-RAY DIFFRACTIONf_dihedral_angle_d6.826921
X-RAY DIFFRACTIONf_chiral_restr0.051222
X-RAY DIFFRACTIONf_plane_restr0.005254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5534-1.59220.22861360.2282496X-RAY DIFFRACTION97
1.5922-1.63530.21161370.19772548X-RAY DIFFRACTION100
1.6353-1.68340.22411410.18382584X-RAY DIFFRACTION100
1.6834-1.73770.18521390.17432569X-RAY DIFFRACTION100
1.7377-1.79980.20861390.17562588X-RAY DIFFRACTION100
1.7998-1.87190.17661400.16482585X-RAY DIFFRACTION100
1.8719-1.95710.19391420.16732619X-RAY DIFFRACTION100
1.9571-2.06030.19111410.16842612X-RAY DIFFRACTION100
2.0603-2.18940.2011430.16342617X-RAY DIFFRACTION100
2.1894-2.35840.21931410.17452625X-RAY DIFFRACTION100
2.3584-2.59570.18171440.17912669X-RAY DIFFRACTION100
2.5957-2.97130.17461480.17332716X-RAY DIFFRACTION100
2.9713-3.74320.16081470.15992722X-RAY DIFFRACTION100
3.7432-46.16560.19591620.17742991X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.1205 Å / Origin y: -5.2842 Å / Origin z: 12.6288 Å
111213212223313233
T0.1526 Å20.0147 Å2-0.0038 Å2-0.1294 Å20.0327 Å2--0.1254 Å2
L0.7996 °2-0.7048 °20.0003 °2-2.434 °20.2863 °2--1.3936 °2
S0.0178 Å °0.0041 Å °0.0323 Å °-0.0833 Å °0.0034 Å °0.0215 Å °-0.0664 Å °-0.0127 Å °-0.003 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 4 through 900)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more