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- PDB-2hl1: Crystal structure of the editing domain of threonyl-tRNA syntheta... -

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Basic information

Entry
Database: PDB / ID: 2hl1
TitleCrystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with seryl-3'-aminoadenosine
ComponentsThreonyl-tRNA synthetase
KeywordsLIGASE / translation / editing / aminoacyl-tRNA synthetase / enzyme mechanism / enantioselectivity
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE-3'-AMINOADENOSINE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHussain, T. / Kruparani, S.P. / Pal, B. / Sankaranarayanan, R.
Citation
Journal: Embo J. / Year: 2006
Title: Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea
Authors: Hussain, T. / Kruparani, S.P. / Pal, B. / Dock-Bregeon, A.C. / Dwivedi, S. / Shekar, M.R. / Sureshbabu, K. / Sankaranarayanan, R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A D-amino acid editing module coupled to the translational apparatus in archaea
Authors: Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonyl-tRNA synthetase
B: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1834
Polymers33,4772
Non-polymers7072
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-2 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.991, 75.735, 95.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

#1: Protein Threonyl-tRNA synthetase / Threonine--tRNA ligase / ThrRS


Mass: 16738.312 Da / Num. of mol.: 2 / Fragment: editing domain (residues 1-147)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-A3S / SERINE-3'-AMINOADENOSINE / N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE


Mass: 353.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 3350, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2005 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. all: 13321 / Num. obs: 13321 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.82
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1201 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y2Q

1y2q


Resolution: 2.25→24.4 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1433959.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 669 5 %RANDOM
Rwork0.205 ---
obs0.205 13293 90.6 %-
all-13293 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7539 Å2 / ksol: 0.33344 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--4.54 Å20 Å2
3----5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.25→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 50 239 2592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 107 5.4 %
Rwork0.245 1885 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3a3s.parama3s.top

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