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- PDB-6z81: TsaBD bound to the inhibitor -

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Basic information

Entry
Database: PDB / ID: 6z81
TitleTsaBD bound to the inhibitor
Components
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsRNA BINDING PROTEIN / tRNA TsaB TsaD
Function / homology
Function and homology information


glycosylation-dependent protein binding / N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / maintenance of translational fidelity / metallopeptidase activity / iron ion binding / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Chem-QCB / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMissoury, S. / Van Tilbeurgh, H.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli.
Authors: Kopina, B.J. / Missoury, S. / Collinet, B. / Fulton, M.G. / Cirio, C. / van Tilbeurgh, H. / Lauhon, C.T.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: tRNA N6-adenosine threonylcarbamoyltransferase
B: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,16933
Polymers125,8264
Non-polymers3,34429
Water1,78399
1
A: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,73819
Polymers62,9132
Non-polymers1,82517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-72 kcal/mol
Surface area22690 Å2
MethodPISA
2
B: tRNA N6-adenosine threonylcarbamoyltransferase
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,43214
Polymers62,9132
Non-polymers1,51912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-51 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.230, 69.250, 86.540
Angle α, β, γ (deg.)109.380, 92.000, 116.940
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 36879.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tsaD, gcp, ygjD, b3064, JW3036
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05852, N6-L-threonylcarbamoyladenine synthase
#2: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / YeaZ / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB


Mass: 26033.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tsaB, yeaZ, b1807, JW1796
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P76256

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Non-polymers , 9 types, 128 molecules

#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-QCB / (2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid


Mass: 490.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23N6O10P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.25 mM Lithium sulfate, 0.11 M Hepes pH 7.5 0.15 mM sodium acetate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.999881 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999881 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 51130 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.21 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.137 / Net I/σ(I): 7.48
Reflection shellResolution: 2.31→2.33 Å / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1023 / CC1/2: 0.79 / Rrim(I) all: 0.63 / % possible all: 54.57

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDU

4ydu


Resolution: 2.31→42.47 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2557 5 %RANDOM
Rwork0.182 ---
obs0.185 51130 96.2 %-
Displacement parametersBiso max: 130.1 Å2 / Biso mean: 38.66 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-1.6987 Å23.4613 Å20.1722 Å2
2--0.3232 Å2-9.1711 Å2
3----2.0219 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.31→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 198 91 8857
Biso mean--51.09 33.37 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3002SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1546HARMONIC5
X-RAY DIFFRACTIONt_it8953HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1171SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10220SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8953HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12169HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion19.52
LS refinement shellResolution: 2.31→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2383 51 4.99 %
Rwork0.2728 972 -
all0.2712 1023 -
obs--54.56 %

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