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- PDB-9dsw: Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) ... -

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Basic information

Entry
Database: PDB / ID: 9dsw
TitleThermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with L-threonine
ComponentsThreonylcarbamoyl-AMP synthase
KeywordsBIOSYNTHETIC PROTEIN / TsaC2 / TsaC / t6A / N6-threonylcarbamoyl adenosine / t6A37 / tRNA / transfer-RNA / reaction intermediate / TC-AMP
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / regulation of translational fidelity / nucleotidyltransferase activity / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
tRNA threonylcarbamoyladenosine biosynthesis protein SUA5 / Threonylcarbamoyl-AMP synthase, C-terminal domain / Threonylcarbamoyl-AMP synthase, C-terminal domain superfamily / Threonylcarbamoyl-AMP synthase, C-terminal domain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase RibB-like alpha/beta domain superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / THREONINE / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsKutshuashvili, A. / Swairjo, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110588 United States
CitationJournal: To Be Published
Title: Crystallographic evidence of N-carboxy-L-threonine intermediate in t6A modification of tRNA.
Authors: Kutchaushvili, A. / Wood, E. / Luthra, A. / Hung, S.-H. / Swinehart, W. / Sankaran, B. / Scheleen, E. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionSep 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonylcarbamoyl-AMP synthase
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,66513
Polymers76,7162
Non-polymers94911
Water4,089227
1
A: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5954
Polymers38,3581
Non-polymers2373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0709
Polymers38,3581
Non-polymers7128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.672, 153.672, 86.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Threonylcarbamoyl-AMP synthase / TC-AMP synthase / L-threonylcarbamoyladenylate synthase


Mass: 38357.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0852 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZV6, L-threonylcarbamoyladenylate synthase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 14% PEG8000, 20% glycerol, 150 mM calcium acetate, 80 mM sodium cacodylate, pH 6.5, 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 1 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.05→44.5 Å / Num. obs: 73986 / % possible obs: 99.9 % / Redundancy: 35.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.04 / Rrim(I) all: 0.247 / Net I/σ(I): 16
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.87 / Num. unique obs: 3656 / CC1/2: 0.366 / Rpim(I) all: 0.04 / Rrim(I) all: 0.247

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→44.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.011 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20183 3283 4.9 %RANDOM
Rwork0.18932 ---
obs0.18993 64297 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.05→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 63 227 5434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165349
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.8627192
X-RAY DIFFRACTIONr_angle_other_deg0.4641.76512390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.391534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89310974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2827
X-RAY DIFFRACTIONr_gen_planes_refined00.025937
X-RAY DIFFRACTIONr_gen_planes_other00.021063
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_it2.4863.0042592
X-RAY DIFFRACTIONr_mcbond_other2.4813.0022588
X-RAY DIFFRACTIONr_mcangle_it3.9985.3883225
X-RAY DIFFRACTIONr_mcangle_other3.9975.3873226
X-RAY DIFFRACTIONr_scbond_it3.3573.5292728
X-RAY DIFFRACTIONr_scbond_other3.3563.5292729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5476.2393967
X-RAY DIFFRACTIONr_long_range_B_refined7.60629.895742
X-RAY DIFFRACTIONr_long_range_B_other7.60529.895743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å
RfactorNum. reflection% reflection
Rfree0.315 111 -
Rwork0.303 2290 -
obs--44.15 %

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