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

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Basic information

Entry
Database: PDB / ID: 9dsv
TitleThermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium and ATP
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 / ADENOSINE-5'-TRIPHOSPHATE / DIPHOSPHATE / threonylcarbamoyladenylate / N-carboxy-L-threonine / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 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 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,00814
Polymers76,7162
Non-polymers2,29212
Water3,819212
1
A: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1716
Polymers38,3581
Non-polymers8135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8378
Polymers38,3581
Non-polymers1,4797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.596, 153.596, 86.553
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
Details: The N-terminal sequence GSHMAS is left over from a thrombin cleavage site after His6 tag removal.
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 , 7 types, 224 molecules

#2: Chemical ChemComp-U6A / N-carboxy-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 163.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-TXA / threonylcarbamoyladenylate


Mass: 492.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N6O11P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.87 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 13.5% PEG8000, 20% glycerol, 230 mM sodium acetate, 80 mM sodium cacodylate, pH 7.4, 25 mg/ml TmTsaC2, 10 mM threonine, 30 mM NaHCO3.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.01→44.38 Å / Num. obs: 78278 / % possible obs: 100 % / Redundancy: 15.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.063 / Rrim(I) all: 0.252 / Net I/σ(I): 10.7
Reflection shellResolution: 2.01→2.05 Å / Redundancy: 16.1 % / Rmerge(I) obs: 4.044 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4436 / CC1/2: 0.308 / Rpim(I) all: 1.032 / Rrim(I) all: 4.175 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
REFMAC5.8.0430phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→44.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.056 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21647 3941 5 %RANDOM
Rwork0.19331 ---
obs0.19446 74298 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: 1 / Resolution: 2.01→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 144 212 5498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165511
X-RAY DIFFRACTIONr_angle_refined_deg1.271.8637592
X-RAY DIFFRACTIONr_angle_other_deg0.4361.76412784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.449535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.462101012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021111
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_it6.8254.2672672
X-RAY DIFFRACTIONr_mcbond_other6.7954.2632668
X-RAY DIFFRACTIONr_mcangle_it8.5427.6573355
X-RAY DIFFRACTIONr_mcangle_other8.5427.6583356
X-RAY DIFFRACTIONr_scbond_it9.30452899
X-RAY DIFFRACTIONr_scbond_other9.3035.0012900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.9418.8044233
X-RAY DIFFRACTIONr_long_range_B_refined13.41541.736034
X-RAY DIFFRACTIONr_long_range_B_other13.41541.736035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 307 -
Rwork0.343 5411 -
obs--99.95 %

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