[English] 日本語
Yorodumi
- PDB-3hj4: Minor Editosome-Associated TUTase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hj4
TitleMinor Editosome-Associated TUTase 1
ComponentsMinor Editosome-Associated TUTase
KeywordsTRANSFERASE / TUTase / nucleotidyltransferase / trypanosoma / editosome / RNA editing / UTP-binding
Function / homology
Function and homology information


RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear lumen / ciliary plasm / DNA-templated transcription / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Poly(a)-polymerase, middle domain - #10 / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA uridylyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsStagno, J. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the Mitochondrial Editosome-Like Complex Associated TUTase 1 Reveals Divergent Mechanisms of UTP Selection and Domain Organization.
Authors: Stagno, J. / Aphasizheva, I. / Bruystens, J. / Luecke, H. / Aphasizhev, R.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Minor Editosome-Associated TUTase
B: Minor Editosome-Associated TUTase


Theoretical massNumber of molelcules
Total (without water)89,6442
Polymers89,6442
Non-polymers00
Water15,835879
1
A: Minor Editosome-Associated TUTase


Theoretical massNumber of molelcules
Total (without water)44,8221
Polymers44,8221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Minor Editosome-Associated TUTase


Theoretical massNumber of molelcules
Total (without water)44,8221
Polymers44,8221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.208, 102.027, 66.074
Angle α, β, γ (deg.)90.000, 111.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 382
2116B1 - 382

-
Components

#1: Protein Minor Editosome-Associated TUTase


Mass: 44821.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.1.1330 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q4GZ86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 291 K / pH: 8
Details: 0.2M lithium acetate, 25% PEG 3350, pH 8.0, vapor diffusion, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.56→99 Å / Num. obs: 108380 / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.181
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 3 % / Rmerge(I) obs: 0.531 / % possible all: 90.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→31.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 3.811 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5426 5 %RANDOM
Rwork0.162 ---
obs0.164 108165 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å22.09 Å2
2---1.29 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.56→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 0 879 7061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226391
X-RAY DIFFRACTIONr_bond_other_d0.0010.024465
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9478651
X-RAY DIFFRACTIONr_angle_other_deg0.923310789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69823.133332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.232151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9531562
X-RAY DIFFRACTIONr_chiral_restr0.0810.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.53852
X-RAY DIFFRACTIONr_mcbond_other0.3831.51552
X-RAY DIFFRACTIONr_mcangle_it1.81326248
X-RAY DIFFRACTIONr_scbond_it2.99632539
X-RAY DIFFRACTIONr_scangle_it4.6654.52392
X-RAY DIFFRACTIONr_rigid_bond_restr1.362310856
X-RAY DIFFRACTIONr_sphericity_free5.0663879
X-RAY DIFFRACTIONr_sphericity_bonded2.077310702
Refine LS restraints NCS

Ens-ID: 1 / Number: 5267 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.345
2Bloose thermal1.4310
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 355 -
Rwork0.289 6883 -
obs--89.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35170.1744-0.25270.6454-0.31170.28410.0066-0.00390.02740.040.01770.0465-0.0244-0.0068-0.02420.02720.0034-0.01640.028-0.00360.01960.21314.24322.0128
20.37390.134-0.2220.2121-0.01510.24650.00150.0123-0.0245-0.0097-0.0048-0.00710.00350.00840.00330.02180.0055-0.01830.0311-0.00240.017822.755138.892728.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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