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- PDB-8iey: Aquifex aeolicus TsaD-TsaB -

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Basic information

Entry
Database: PDB / ID: 8iey
TitleAquifex aeolicus TsaD-TsaB
Components
  • Gcp-like domain-containing protein
  • tRNA N6-adenosine threonylcarbamoyltransferase
KeywordsTRANSFERASE / tRNA t6A-modifying enzyme / TsaD-TsaB complex
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytoplasm / cytosol
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / 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
: / DI(HYDROXYETHYL)ETHER / Gcp-like domain-containing protein / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLu, S.Z. / Zhang, W.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000847 China
CitationJournal: To Be Published
Title: Crystal structure of Aquifex aeolicus TsaD-TsaB complex
Authors: Lu, S.Z. / Zhang, W.H.
History
DepositionFeb 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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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: Gcp-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0938
Polymers60,5072
Non-polymers5866
Water4,288238
1
A: tRNA N6-adenosine threonylcarbamoyltransferase
B: Gcp-like domain-containing protein
hetero molecules

A: tRNA N6-adenosine threonylcarbamoyltransferase
B: Gcp-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18716
Polymers121,0144
Non-polymers1,17312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area10970 Å2
ΔGint-45 kcal/mol
Surface area39600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.719, 97.719, 132.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Components on special symmetry positions
IDModelComponents
11B-455-

HOH

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Components

#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: 37433.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: tsaD, gcp, aq_801
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O66986, N6-L-threonylcarbamoyladenine synthase
#2: Protein Gcp-like domain-containing protein / TsaB


Mass: 23073.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_082
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O66494
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9 mg/ml TsaD-TsaB, 0.1 M MES pH 6.5, 30 % PEG 300, 200 mM NaC

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Data collection

DiffractionMean temperature: 150 K / Ambient temp details: Liquid nitrogen gas flow / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 27, 2021 / Details: CMF
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→30.64 Å / Num. obs: 48654 / % possible obs: 99.9 % / Redundancy: 24.5 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.103 / Net I/σ(I): 30.87
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 4427 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisPro1.1.11data reduction
Aimless1.12.15data scaling
Coot0.9.8.7model building
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.52 Å / SU ML: 0.2819 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.2282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 2434 5.03 %RANDOM
Rwork0.2164 45943 --
obs0.219 48377 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.65 Å2
Refinement stepCycle: LAST / Resolution: 2→30.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 36 238 4408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794266
X-RAY DIFFRACTIONf_angle_d0.90745767
X-RAY DIFFRACTIONf_chiral_restr0.057646
X-RAY DIFFRACTIONf_plane_restr0.008727
X-RAY DIFFRACTIONf_dihedral_angle_d8.9227582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.38491680.36072468X-RAY DIFFRACTION91.66
2.04-2.090.50871560.42262513X-RAY DIFFRACTION91.66
2.09-2.130.43751120.36812601X-RAY DIFFRACTION94.01
2.13-2.190.24371570.23752738X-RAY DIFFRACTION99.97
2.19-2.250.45341140.3842428X-RAY DIFFRACTION87.87
2.25-2.310.44551440.38182504X-RAY DIFFRACTION90.5
2.31-2.390.29251420.21752748X-RAY DIFFRACTION99.93
2.39-2.470.24151220.20622759X-RAY DIFFRACTION99.69
2.47-2.570.25271630.20412771X-RAY DIFFRACTION99.63
2.57-2.690.27561310.21432735X-RAY DIFFRACTION98.62
2.69-2.830.25891450.20622734X-RAY DIFFRACTION99
2.83-3.010.26051460.212774X-RAY DIFFRACTION99.73
3.01-3.240.26291290.19292803X-RAY DIFFRACTION99.39
3.24-3.560.24941320.19512786X-RAY DIFFRACTION99.05
3.56-4.080.22141580.16852794X-RAY DIFFRACTION99.09
4.08-5.130.18671770.15492820X-RAY DIFFRACTION99.6
5.14-30.520.2271380.1832967X-RAY DIFFRACTION99.87

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