[English] 日本語
Yorodumi
- PDB-2q0f: Terminal uridylyl transferase 4 from Trypanosoma brucei with boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q0f
TitleTerminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UMP
ComponentsRNA uridylyl transferase
KeywordsTRANSFERASE / TUTase / Trypanosoma / nucleotidyltransferase / UTP-binding / RNA-editing
Function / homology
Function and homology information


RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / kinetoplast / nucleotide binding / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase 4
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStagno, J. / Luecke, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.
Authors: Stagno, J. / Aphasizheva, I. / Aphasizhev, R. / Luecke, H.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA uridylyl transferase
B: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9407
Polymers79,7592
Non-polymers1,1815
Water3,315184
1
A: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7365
Polymers39,8791
Non-polymers8574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2042
Polymers39,8791
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.620, 41.924, 106.017
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein RNA uridylyl transferase / RNA uridylyltransferase 4


Mass: 39879.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: TUT4 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q381M1, RNA uridylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 200 mM calcium acetate, 18% PEG-8000, 4 mM MgCl2, 50 uM UTP, crystals soaked in 10 mM UMP for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979 Å
DetectorDate: Jul 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→41.92 Å / Num. obs: 26495 / % possible obs: 93.8 % / Redundancy: 3.38 % / Rmerge(I) obs: 0.14 / Χ2: 0.99 / Net I/σ(I): 6.4 / Scaling rejects: 677
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.493.480.4762.3912726101.0693
2.49-2.593.460.462.4909126181.0793.7
2.59-2.73.450.4342.5900526001.0593.6
2.7-2.853.430.42.7908126281.1193.8
2.85-3.023.360.3413895126421.0294.6
3.02-3.263.320.2723.5887926600.9694.4
3.26-3.583.230.1745851626200.9993.5
3.58-4.13.230.1127.8838025670.9590.6
4.1-5.173.250.06712.6874126550.8692.8
5.17-41.923.570.04520.21043128950.8697.8

-
Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-IceIcedata collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IKF

2ikf


Resolution: 2.4→38.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.733 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.683 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1364 5.1 %test set taken from 2IKF
Rwork0.223 ---
obs0.226 26486 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 73 184 5389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225318
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9717225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65823.187251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00415891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7651547
X-RAY DIFFRACTIONr_chiral_restr0.0960.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024004
X-RAY DIFFRACTIONr_nbd_refined0.2240.22383
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.29
X-RAY DIFFRACTIONr_mcbond_it0.6541.53281
X-RAY DIFFRACTIONr_mcangle_it1.15125180
X-RAY DIFFRACTIONr_scbond_it1.43632300
X-RAY DIFFRACTIONr_scangle_it2.3014.52045
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 101 -
Rwork0.289 1848 -
obs-1949 92.5 %

+
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