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- PDB-3ugt: Crystal structure of the yeast mitochondrial threonyl-tRNA synthe... -

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Basic information

Entry
Database: PDB / ID: 3ugt
TitleCrystal structure of the yeast mitochondrial threonyl-tRNA synthetase - orthorhombic crystal form
ComponentsThreonyl-tRNA synthetase, mitochondrial
KeywordsLIGASE / threonyl-tRNA synthetase / aminoacyl-tRNA synthetase class II / yeast mitochondrial threonine tRNA 1 and 2
Function / homology
Function and homology information


mitochondrial threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / mitochondrial matrix / mitochondrion / ATP binding
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / Anticodon-binding domain / 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 / Bira Bifunctional Protein; Domain 2 ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / Anticodon-binding domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Threonine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPeterson, K.M. / Ling, J. / Simonovic, I. / Cho, C. / Soll, D. / Simonovic, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment.
Authors: Ling, J. / Peterson, K.M. / Simonovic, I. / Cho, C. / Soll, D. / Simonovic, M.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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, mitochondrial
B: Threonyl-tRNA synthetase, mitochondrial
C: Threonyl-tRNA synthetase, mitochondrial
D: Threonyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1578
Polymers213,8964
Non-polymers2624
Water82946
1
A: Threonyl-tRNA synthetase, mitochondrial
B: Threonyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0794
Polymers106,9482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-123 kcal/mol
Surface area34780 Å2
MethodPISA
2
C: Threonyl-tRNA synthetase, mitochondrial
D: Threonyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0794
Polymers106,9482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-125 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.083, 157.939, 237.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 53473.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / Gene: MST1, YKL194C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: P07236, threonine-tRNA ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M magnesium formate, 20% PEG 3.350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 33252 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.162 / Net I/σ(I): 10.7
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.73 / Num. unique all: 1411 / Rsym value: 0.802 / % possible all: 83.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→35.113 Å / SU ML: 0.5 / σ(F): 0 / σ(I): 0 / Phase error: 28.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1634 4.96 %thin shells
Rwork0.2372 ---
obs0.2391 32952 97.47 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.828 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.1352 Å20 Å2-0 Å2
2--10.7125 Å20 Å2
3----22.8477 Å2
Refinement stepCycle: LAST / Resolution: 3.6→35.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13388 0 4 46 13438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514233
X-RAY DIFFRACTIONf_angle_d0.72918720
X-RAY DIFFRACTIONf_dihedral_angle_d10.9845013
X-RAY DIFFRACTIONf_chiral_restr0.0562010
X-RAY DIFFRACTIONf_plane_restr0.0032445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70580.37061110.3262253X-RAY DIFFRACTION85
3.7058-3.82530.35871270.30262428X-RAY DIFFRACTION92
3.8253-3.96180.34811250.29922575X-RAY DIFFRACTION96
3.9618-4.12020.28441260.26672602X-RAY DIFFRACTION99
4.1202-4.30740.30081360.25072647X-RAY DIFFRACTION99
4.3074-4.53410.29591360.23212643X-RAY DIFFRACTION99
4.5341-4.81750.24351480.21292667X-RAY DIFFRACTION100
4.8175-5.18840.26411410.21482633X-RAY DIFFRACTION100
5.1884-5.70850.26521430.23412676X-RAY DIFFRACTION100
5.7085-6.52990.34821370.26042701X-RAY DIFFRACTION100
6.5299-8.20960.26591420.23362713X-RAY DIFFRACTION100
8.2096-35.11490.20091620.18952780X-RAY DIFFRACTION99

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