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- PDB-5gha: Sulfur Transferase TtuA in complex with Sulfur Carrier TtuB -

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Basic information

Entry
Database: PDB / ID: 5gha
TitleSulfur Transferase TtuA in complex with Sulfur Carrier TtuB
Components
  • Sulfur Carrier TtuB
  • Sulfur Transferase TtuA
KeywordsTRANSFERASE/TRANSPORT PROTEIN / sulfur transferase / TRANSFERASE / TRANSFERASE-TRANSPORT PROTEIN 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
tRNA-5-methyluridine(54) 2-sulfurtransferase / Sulfur carrier protein TtuB
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.502 Å
AuthorsChen, M. / Narai, S. / Tanaka, Y. / Yao, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA
Authors: Chen, M. / Asai, S. / Narai, S. / Nambu, S. / Omura, N. / Sakaguchi, Y. / Suzuki, T. / Ikeda-Saito, M. / Watanabe, K. / Yao, M. / Shigi, N. / Tanaka, Y.
History
DepositionJun 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfur Transferase TtuA
D: Sulfur Transferase TtuA
B: Sulfur Transferase TtuA
C: Sulfur Transferase TtuA
E: Sulfur Carrier TtuB
H: Sulfur Carrier TtuB
F: Sulfur Carrier TtuB
G: Sulfur Carrier TtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,34025
Polymers183,1568
Non-polymers1,18417
Water1,45981
1
A: Sulfur Transferase TtuA
B: Sulfur Transferase TtuA
E: Sulfur Carrier TtuB
F: Sulfur Carrier TtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,21813
Polymers91,5784
Non-polymers6409
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-52 kcal/mol
Surface area35900 Å2
MethodPISA
2
D: Sulfur Transferase TtuA
C: Sulfur Transferase TtuA
H: Sulfur Carrier TtuB
G: Sulfur Carrier TtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,12212
Polymers91,5784
Non-polymers5448
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-44 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.139, 93.873, 97.532
Angle α, β, γ (deg.)109.21, 104.57, 106.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ADBCEHFG

#1: Protein
Sulfur Transferase TtuA / Veg136 protein


Mass: 36252.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: TT_C0106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LF3
#2: Protein
Sulfur Carrier TtuB / Uncharacterized protein


Mass: 9536.782 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: G65C mutant / Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: TT_C0105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LF4

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Non-polymers , 4 types, 98 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M HEPES-NaOH, 0-20%(v/v) PEG6000 / PH range: 6.2-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.28251, 1.28311, 1.00000
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.282511
21.283111
311
ReflectionResolution: 2.5→47.84 Å / Num. obs: 105373 / % possible obs: 94.9 % / Redundancy: 1.97 % / Net I/σ(I): 16.24

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RESOLVEphasing
RESOLVEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.502→47.84 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2752 5.11 %
Rwork0.1955 --
obs0.1981 53904 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11721 0 47 81 11849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311934
X-RAY DIFFRACTIONf_angle_d0.67816050
X-RAY DIFFRACTIONf_dihedral_angle_d13.454628
X-RAY DIFFRACTIONf_chiral_restr0.0241794
X-RAY DIFFRACTIONf_plane_restr0.0032071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5018-2.5450.32571330.25092428X-RAY DIFFRACTION93
2.545-2.59120.32521320.23862590X-RAY DIFFRACTION96
2.5912-2.64110.32451410.22692476X-RAY DIFFRACTION97
2.6411-2.6950.30181330.22312584X-RAY DIFFRACTION96
2.695-2.75360.30851440.22912503X-RAY DIFFRACTION97
2.7536-2.81760.32431260.2362560X-RAY DIFFRACTION97
2.8176-2.88810.29081290.22872551X-RAY DIFFRACTION97
2.8881-2.96610.30521140.23432549X-RAY DIFFRACTION97
2.9661-3.05340.26931470.232561X-RAY DIFFRACTION97
3.0534-3.15190.31581330.23272582X-RAY DIFFRACTION98
3.1519-3.26460.27561780.22582516X-RAY DIFFRACTION98
3.2646-3.39520.27531320.2172578X-RAY DIFFRACTION98
3.3952-3.54970.27281150.19442578X-RAY DIFFRACTION98
3.5497-3.73680.20691390.18892574X-RAY DIFFRACTION98
3.7368-3.97080.22611410.18772575X-RAY DIFFRACTION98
3.9708-4.27720.22631660.17272590X-RAY DIFFRACTION99
4.2772-4.70730.22031280.15522581X-RAY DIFFRACTION98
4.7073-5.38770.21721330.16852611X-RAY DIFFRACTION99
5.3877-6.78480.21981490.20592591X-RAY DIFFRACTION99
6.7848-47.84860.19741390.16742574X-RAY DIFFRACTION98

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