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- PDB-6f87: Crystal structure of P. abyssi Sua5 complexed with L-threonine and PPi -

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Basic information

Entry
Database: PDB / ID: 6f87
TitleCrystal structure of P. abyssi Sua5 complexed with L-threonine and PPi
ComponentsThreonylcarbamoyl-AMP synthase
KeywordsTRANSFERASE / Nucleotidyltransferase / tRNA modification / threonylcarbamoylation
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / double-stranded RNA 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 / DHBP synthase RibB-like alpha/beta domain superfamily ...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 / DHBP synthase RibB-like alpha/beta domain superfamily / DHBP synthase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / THREONINE / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPichard-Kostuch, A. / Zhang, W. / Liger, D. / Daugeron, M.C. / Letoquart, J. / Li de la Sierra-Gallay, I. / Forterre, P. / Collinet, B. / van Tilbeurgh, H. / Basta, T.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Structural BiologyFRISBI ANR-10-INSB-050 France
CitationJournal: RNA / Year: 2018
Title: Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification.
Authors: Pichard-Kostuch, A. / Zhang, W. / Liger, D. / Daugeron, M.C. / Letoquart, J. / Li de la Sierra-Gallay, I. / Forterre, P. / Collinet, B. / van Tilbeurgh, H. / Basta, T.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,96912
Polymers152,7894
Non-polymers1,1808
Water1,838102
1
A: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4923
Polymers38,1971
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4923
Polymers38,1971
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4923
Polymers38,1971
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4923
Polymers38,1971
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.440, 144.070, 103.660
Angle α, β, γ (deg.)90.000, 103.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-529-

HOH

21D-526-

HOH

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Components

#1: Protein
Threonylcarbamoyl-AMP synthase / TC-AMP synthase / L-threonylcarbamoyladenylate synthase / t(6)A37 threonylcarbamoyladenosine ...TC-AMP synthase / L-threonylcarbamoyladenylate synthase / t(6)A37 threonylcarbamoyladenosine biosynthesis protein Sua5 / tRNA threonylcarbamoyladenosine biosynthesis protein Sua5


Mass: 38197.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: sua5, PYRAB15960, PAB1302 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UYB2, L-threonylcarbamoyladenylate synthase
#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O7P2
#3: Chemical
ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate / PH range: 8.5 - 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.62→49.03 Å / Num. obs: 64452 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rrim(I) all: 0.071 / Net I/σ(I): 14.14
Reflection shellResolution: 2.62→2.78 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 10212 / Rrim(I) all: 0.69 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EQA

2eqa


Resolution: 2.62→49.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.58 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3223 5 %RANDOM
Rwork0.1754 ---
obs0.1781 61225 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 236.33 Å2 / Biso mean: 66.881 Å2 / Biso min: 35.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.62→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 68 102 10730
Biso mean--58.12 54.01 -
Num. residues----1360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910824
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210852
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.98814648
X-RAY DIFFRACTIONr_angle_other_deg1.051325032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82851356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93223.273440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.285151948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1151592
X-RAY DIFFRACTIONr_chiral_restr0.0940.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022212
LS refinement shellResolution: 2.617→2.685 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 229 -
Rwork0.319 4352 -
all-4581 -
obs--95.1 %

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