[English] 日本語
Yorodumi
- PDB-5ztb: Structure of Sulfurtransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ztb
TitleStructure of Sulfurtransferase
Components
  • Sulfur carrier protein TtuB
  • tRNA-5-methyluridine(54) 2-sulfurtransferase
KeywordsRNA BINDING PROTEIN/TRANSFERASE / Sulfur transfer / iron-sulfur cluster / tRNA binding protein / complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


tRNA-5-methyluridine54 2-sulfurtransferase / tRNA thio-modification / tRNA wobble uridine modification / tRNA processing / 4 iron, 4 sulfur cluster binding / transferase activity / tRNA binding / nucleotide binding / ATP binding / metal ion binding
Similarity search - Function
Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / IRON/SULFUR CLUSTER / tRNA-5-methyluridine(54) 2-sulfurtransferase / Sulfur carrier protein TtuB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTanaka, Y. / Chen, M. / Narai, S. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15J01961 Japan
CitationJournal: Commun Biol / Year: 2020
Title: The [4Fe-4S] cluster of sulfurtransferase TtuA desulfurizes TtuB during tRNA modification in Thermus thermophilus.
Authors: Chen, M. / Ishizaka, M. / Narai, S. / Horitani, M. / Shigi, N. / Yao, M. / Tanaka, Y.
History
DepositionMay 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Sulfur carrier protein TtuB
B: tRNA-5-methyluridine(54) 2-sulfurtransferase
D: Sulfur carrier protein TtuB
A: tRNA-5-methyluridine(54) 2-sulfurtransferase
F: Sulfur carrier protein TtuB
C: tRNA-5-methyluridine(54) 2-sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,62826
Polymers133,8956
Non-polymers3,73320
Water2,000111
1
E: Sulfur carrier protein TtuB
B: tRNA-5-methyluridine(54) 2-sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09811
Polymers44,6322
Non-polymers1,4669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-76 kcal/mol
Surface area18380 Å2
MethodPISA
2
D: Sulfur carrier protein TtuB
A: tRNA-5-methyluridine(54) 2-sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7177
Polymers44,6322
Non-polymers1,0865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-46 kcal/mol
Surface area18470 Å2
MethodPISA
3
F: Sulfur carrier protein TtuB
C: tRNA-5-methyluridine(54) 2-sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8138
Polymers44,6322
Non-polymers1,1826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-60 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.622, 82.770, 138.495
Angle α, β, γ (deg.)90.00, 115.86, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 6 molecules EDFBAC

#1: Protein Sulfur carrier protein TtuB / 2-thiouridine synthesis sulfur carrier protein TtuB / Ubiquitin-like S-donor protein TtuB / ...2-thiouridine synthesis sulfur carrier protein TtuB / Ubiquitin-like S-donor protein TtuB / Ubiquitin-like protein modifier TtuB / tRNA two-thiouridine-synthesizing protein B


Mass: 8379.415 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: ttuB, TT_C0105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LF4
#2: Protein tRNA-5-methyluridine(54) 2-sulfurtransferase / 2-thiouridine synthetase TtuA / tRNA two-thiouridine-synthesizing protein A


Mass: 36252.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: ttuA, TT_C0106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q72LF3, tRNA-5-methyluridine54 2-sulfurtransferase

-
Non-polymers , 6 types, 131 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15 M ammonium sulfate, 0.1 M Tris pH 8.0, 15%(w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.901 Å / Num. obs: 84554 / % possible obs: 98.3 % / Redundancy: 3.46 % / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.32 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.901 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.59
RfactorNum. reflection% reflection
Rfree0.2409 4197 4.97 %
Rwork0.2155 --
obs0.2168 84477 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8894 0 164 111 9169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089221
X-RAY DIFFRACTIONf_angle_d0.86312450
X-RAY DIFFRACTIONf_dihedral_angle_d13.2743588
X-RAY DIFFRACTIONf_chiral_restr0.031384
X-RAY DIFFRACTIONf_plane_restr0.0041582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.35491360.29692604X-RAY DIFFRACTION97
2.225-2.25120.31331370.28812627X-RAY DIFFRACTION97
2.2512-2.27860.32991360.28692634X-RAY DIFFRACTION98
2.2786-2.30750.34421410.28452705X-RAY DIFFRACTION99
2.3075-2.33780.32211390.26842671X-RAY DIFFRACTION99
2.3378-2.36990.26491430.26672730X-RAY DIFFRACTION99
2.3699-2.40370.31761380.26612624X-RAY DIFFRACTION99
2.4037-2.43960.30491440.25452708X-RAY DIFFRACTION99
2.4396-2.47770.28451380.25332651X-RAY DIFFRACTION99
2.4777-2.51830.29031420.25972683X-RAY DIFFRACTION99
2.5183-2.56170.28541390.25622690X-RAY DIFFRACTION99
2.5617-2.60830.26741410.24582665X-RAY DIFFRACTION99
2.6083-2.65850.28491400.24462685X-RAY DIFFRACTION99
2.6585-2.71270.28331380.24882663X-RAY DIFFRACTION98
2.7127-2.77170.28781380.26042644X-RAY DIFFRACTION97
2.7717-2.83620.33791440.26892673X-RAY DIFFRACTION99
2.8362-2.90710.30211260.25322672X-RAY DIFFRACTION99
2.9071-2.98570.2791520.26222698X-RAY DIFFRACTION99
2.9857-3.07350.29041320.26252687X-RAY DIFFRACTION99
3.0735-3.17270.28521310.25012700X-RAY DIFFRACTION99
3.1727-3.28610.28761470.25672681X-RAY DIFFRACTION99
3.2861-3.41760.2591420.2422684X-RAY DIFFRACTION99
3.4176-3.57310.25131340.22342635X-RAY DIFFRACTION97
3.5731-3.76140.22181410.21152688X-RAY DIFFRACTION99
3.7614-3.99690.24931370.19582694X-RAY DIFFRACTION99
3.9969-4.30530.2161390.18742702X-RAY DIFFRACTION99
4.3053-4.73820.17371480.16872677X-RAY DIFFRACTION98
4.7382-5.42290.20021420.17742651X-RAY DIFFRACTION97
5.4229-6.82870.21181410.19242726X-RAY DIFFRACTION99
6.8287-45.91050.18371510.15992728X-RAY DIFFRACTION97

+
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