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- PDB-6nak: BACTERIAL PROTEIN COMPLEX TM BDE complex -

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Basic information

Entry
Database: PDB / ID: 6nak
TitleBACTERIAL PROTEIN COMPLEX TM BDE complex
Components
  • TsaE
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsRNA BINDING PROTEIN / HETERO-HEXAMER COMPLEX / METAL ION BINDING PROTEINS
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytosol / cytoplasm
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / threonylcarbamoyladenylate / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaE
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsStec, B.
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
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 0THIS ENTRY 6NAK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 6FPE, DETERMINED BY S. ...THIS ENTRY 6NAK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 6FPE, DETERMINED BY S.MISSOURY,S.PLANCQUEEL,I.LI-DE-LA-SIERRA-GALLAY,W.ZHANG,D.LIGER, D.DURAND,R.DAMMAK,B.COLLINET,H.VAN TILBEURGH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
B: tRNA N6-adenosine threonylcarbamoyltransferase
D: TsaE
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
G: tRNA N6-adenosine threonylcarbamoyltransferase
E: TsaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,58814
Polymers160,4136
Non-polymers2,1758
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16610 Å2
ΔGint-155 kcal/mol
Surface area55430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.310, 113.990, 177.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules ACBGDE

#1: 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 MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: tsaB, TM_0874, Tmari_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX7
#2: 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 MSB8 (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
#3: Protein TsaE


Mass: 21513.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TsaE / Production host: Escherichia coli (E. coli) / References: UniProt: R4NRX5

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Non-polymers , 5 types, 12 molecules

#4: Chemical ChemComp-TXA / threonylcarbamoyladenylate


Mass: 492.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N6O11P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.66 Å3/Da / Density % sol: 53.75 % / Description: Author used the sf data from the entry 6FPE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 13 % PEG 8000, 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 2 / Wavelength: 0.981 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 3.14→48.4 Å / Num. obs: 30297 / % possible obs: 99 % / Redundancy: 4.56 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 7.47
Reflection shellResolution: 3.14→3.3 Å / Redundancy: 4.7 % / Num. unique obs: 1505 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fpe

6fpe
PDB Unreleased entry


Resolution: 3.14→48.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.88 / SU B: 78.908 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30166 1550 5.1 %RANDOM
Rwork0.1921 ---
obs0.19772 28747 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 87.322 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---2.03 Å20 Å2
3---0.92 Å2
Refinement stepCycle: 1 / Resolution: 3.14→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10847 0 132 4 10983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311176
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710859
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6515133
X-RAY DIFFRACTIONr_angle_other_deg1.1531.58425201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.11351376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2522.903534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.863152035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5331563
X-RAY DIFFRACTIONr_chiral_restr0.0640.21427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212228
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022163
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_it3.386.825525
X-RAY DIFFRACTIONr_mcbond_other3.386.8195524
X-RAY DIFFRACTIONr_mcangle_it5.63810.226894
X-RAY DIFFRACTIONr_mcangle_other5.63710.226895
X-RAY DIFFRACTIONr_scbond_it3.0687.2095651
X-RAY DIFFRACTIONr_scbond_other3.0687.2095651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.36610.6918240
X-RAY DIFFRACTIONr_long_range_B_refined8.84379.92412205
X-RAY DIFFRACTIONr_long_range_B_other8.84379.92312206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.141→3.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 90 -
Rwork0.4 1932 -
obs--90.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36320.10730.41451.37580.10210.5243-0.12170.0125-0.12550.17340.17720.0716-0.129-0.0556-0.05550.0784-0.01360.06320.31230.08220.3911-56.525845.8204-54.1641
20.7541-0.36940.36840.48270.17080.5992-0.11920.14030.0150.04780.03920.1016-0.06730.20660.080.0252-0.0743-0.01710.40320.1260.3253-19.656436.0283-48.479
31.587-0.0871-0.25830.25850.29440.6070.28730.2457-0.1203-0.0136-0.07260.0666-0.0171-0.0041-0.21470.08220.0368-0.07380.3114-0.07840.3945-35.934918.7785-67.1052
41.2415-0.2745-0.43740.4759-0.20320.385-0.0967-0.0249-0.13260.00750.06490.10610.0390.02750.03180.012-0.03570.01780.36530.04330.3854-66.796560.6789-75.7406
50.7063-0.71960.04770.91870.11710.2428-0.2020.0820.13840.20140.0071-0.1092-0.0282-0.01230.19490.0602-0.0257-0.08130.3091-0.00520.4577-63.171599.2358-79.7904
60.88150.2-0.74040.71820.14561.3317-0.0026-0.098-0.0863-0.05910.1069-0.0116-0.1086-0.1167-0.10430.02150.05180.00510.49590.08910.2388-87.249488.5846-64.7318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 203
2X-RAY DIFFRACTION2B1 - 327
3X-RAY DIFFRACTION3D-3 - 161
4X-RAY DIFFRACTION3D200 - 201
5X-RAY DIFFRACTION4C1 - 206
6X-RAY DIFFRACTION5G1 - 327
7X-RAY DIFFRACTION6E0 - 160
8X-RAY DIFFRACTION6E200 - 201

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