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- PDB-6s84: TsaBDE complex from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 6s84
TitleTsaBDE complex from Thermotoga maritima
Components
  • ATPase YjeE, predicted to have essential role in cell wall biosynthesis
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsRNA BINDING PROTEIN / modification / t6A / tRNA maturation
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #200 / tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Nucleotidyltransferase; domain 5 - #200 / tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / LEUCINE / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsMissoury, S. / Li-de-La-Sierra-Gallay, I. / van Tilbeurgh, H.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification.
Authors: Missoury, S. / Plancqueel, S. / Li de la Sierra-Gallay, I. / Zhang, W. / Liger, D. / Durand, D. / Dammak, R. / Collinet, B. / van Tilbeurgh, H.
History
DepositionJul 8, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionJul 17, 2019ID: 6FPE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA N6-adenosine threonylcarbamoyltransferase
E: ATPase YjeE, predicted to have essential role in cell wall biosynthesis
D: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
F: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
B: ATPase YjeE, predicted to have essential role in cell wall biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,61413
Polymers160,4136
Non-polymers2,2017
Water32418
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16810 Å2
ΔGint-93 kcal/mol
Surface area54000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 108.210, 176.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules ADEBCF

#1: Protein tRNA N6-adenosine threonylcarbamoyltransferase / N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine ...N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD / tRNA threonylcarbamoyladenosine biosynthesis protein TsaD


Mass: 35672.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: tsaD, gcp, TM_0145 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WXZ2, N6-L-threonylcarbamoyladenine synthase
#2: Protein ATPase YjeE, predicted to have essential role in cell wall biosynthesis


Mass: 21513.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1641 / Production host: Escherichia coli (E. coli) / References: UniProt: R4NRX5
#3: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB


Mass: 23020.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: tsaB, TM_0874, Tmari_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX7

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Non-polymers , 4 types, 25 molecules

#4: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 13 % PEG 8000, 0.1 mM Imidazole pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.89→48.43 Å / Num. obs: 36847 / % possible obs: 99.1 % / Redundancy: 8.793 % / Biso Wilson estimate: 80.486 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.199 / Χ2: 1.18 / Net I/σ(I): 9.17 / Num. measured all: 323984
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.89-3.078.5662.2070.8747935590355960.4212.34994.8
3.07-3.289.0951.2781.6250875559455940.7431.356100
3.28-3.548.8750.7062.9545753515551550.8790.75100
3.54-3.888.9110.3655.7742728479547950.9630.387100
3.88-4.338.9210.20210.1938808435143500.9870.215100
4.33-58.7210.12216.2633707386738650.9940.1399.9
5-6.18.9540.1216.429735332133210.9950.127100
6.1-8.568.4750.07422.7722077260526050.9980.078100
8.56-48.437.9010.04538.3212365157815650.9990.04899.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→48.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.904 / SU B: 28.035 / SU ML: 0.465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 1843 5 %RANDOM
Rwork0.2086 ---
obs0.2122 35004 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 227.34 Å2 / Biso mean: 89.656 Å2 / Biso min: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.7 Å2-0 Å2-0 Å2
2--0.93 Å2-0 Å2
3---5.78 Å2
Refinement stepCycle: final / Resolution: 2.89→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10526 0 134 18 10678
Biso mean--101.82 48.55 -
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01210862
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.63714707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08651333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09222.75520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.875151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4281563
X-RAY DIFFRACTIONr_chiral_restr0.0860.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028026
LS refinement shellResolution: 2.894→2.969 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 120 -
Rwork0.442 2274 -
all-2394 -
obs--88.77 %

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