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- PDB-5b4e: Sulfur Transferase TtuA in complex with iron sulfur cluster and A... -

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Basic information

Entry
Database: PDB / ID: 5b4e
TitleSulfur Transferase TtuA in complex with iron sulfur cluster and ATP derivative
ComponentsSulfur Transferase TtuA
KeywordsTRANSFERASE / sulfur transferase
Function / homology
Function and homology information


tRNA-5-methyluridine54 2-sulfurtransferase / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble position uridine thiolation / transferase activity / 4 iron, 4 sulfur cluster binding / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / : / 2-thiouridine synthetase TtuA, N-terminal LIM domain / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ISOPROPYL ALCOHOL / IRON/SULFUR CLUSTER / tRNA-5-methyluridine(54) 2-sulfurtransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.698 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.I. / Narai, S. / Nambu, S. / Omura, N. / Sakaguchi, Y. / Suzuki, T. / Ikeda-Saito, M. / Watanabe, K. / Yao, M. / Shigi, N. / Tanaka, Y.
History
DepositionApr 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references / Structure summary
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

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Assembly

Deposited unit
A: Sulfur Transferase TtuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,93412
Polymers37,3091
Non-polymers1,62511
Water70339
1
A: Sulfur Transferase TtuA
hetero molecules

A: Sulfur Transferase TtuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,86924
Polymers74,6192
Non-polymers3,25022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6460 Å2
ΔGint-204 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.911, 92.911, 266.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfur Transferase TtuA / tRNA sulfur transferase / Veg136 protein


Mass: 37309.359 Da / Num. of mol.: 1
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: TT_C0106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LF3

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Non-polymers , 6 types, 50 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate (pH 3.8-5.6), 30-60%(v/v) 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.35 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35 Å / Relative weight: 1
ReflectionResolution: 2.698→46.5 Å / Num. obs: 35452 / % possible obs: 99.8 % / Redundancy: 7.74 % / Rsym value: 0.086 / Net I/σ(I): 18
Reflection shellResolution: 2.698→2.86 Å / Redundancy: 7.62 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.74 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.698→46.455 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.79
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.237 982 5 %
Rwork0.2156 --
obs0.2167 19640 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.698→46.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 75 39 2513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092521
X-RAY DIFFRACTIONf_angle_d0.9643406
X-RAY DIFFRACTIONf_dihedral_angle_d18.624961
X-RAY DIFFRACTIONf_chiral_restr0.047368
X-RAY DIFFRACTIONf_plane_restr0.004424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.698-2.84020.30541380.26812566X-RAY DIFFRACTION99
2.8402-3.01810.27871360.23362603X-RAY DIFFRACTION100
3.0181-3.25110.22981350.21652607X-RAY DIFFRACTION100
3.2511-3.57820.23321400.19842640X-RAY DIFFRACTION100
3.5782-4.09570.19191400.19592645X-RAY DIFFRACTION100
4.0957-5.15910.2361430.20812715X-RAY DIFFRACTION100
5.1591-46.46240.24991500.22972882X-RAY DIFFRACTION100

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