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- PDB-1nyr: Structure of Staphylococcus aureus threonyl-tRNA synthetase compl... -

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Basic information

Entry
Database: PDB / ID: 1nyr
TitleStructure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP
Componentsthreonyl-tRNA synthetase 1
KeywordsLIGASE / threonyl-tRNA synthetase / ATP / threonine
Function / homology
Function and homology information


catalytic activity, acting on a protein / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / transferase activity / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Threonyl-trna Synthetase; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain ...Threonyl-trna Synthetase; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like / tRNA synthetase class II core domain (G, H, P, S and T) / TGS domain profile. / TGS / Beta-grasp domain / 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. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / THREONINE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTorres-Larios, A. / Sankaranarayanan, R. / Rees, B. / Dock-Bregeon, A.C. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase
Authors: Torres-Larios, A. / Sankaranarayanan, R. / Rees, B. / Dock-Bregeon, A.C. / Moras, D.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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 1
B: threonyl-tRNA synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,5739
Polymers149,1242
Non-polymers1,4497
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-109 kcal/mol
Surface area59530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.130, 122.521, 148.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe protein is a homodimer made of chains A and B

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Components

#1: Protein threonyl-tRNA synthetase 1


Mass: 74562.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pBlue-Pet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8NW68, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.17 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris.Cl, potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMHEPES1droppH7.2
32 mM1dropMgCl2
4100 mM1dropKCl
512-14 %(w/v)PEG80001reservoir
650 mMTris-HCl1reservoirpH7.5-8.5
70.2-0.4 Mammonium acetate1reservoiror KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 1999 / Details: mirrors
RadiationMonochromator: 2 Silicon crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 46973 / Num. obs: 46973 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 79.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.1
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2998 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 160435
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 95.7 % / Num. unique obs: 2998 / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QF6

1qf6


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 2311 5 %RANDOM
Rwork0.239 ---
obs0.239 46618 98.8 %-
all-46618 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.1117 Å2 / ksol: 0.334807 e/Å3
Displacement parametersBiso mean: 73.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.3 Å20 Å20 Å2
2---3.09 Å20 Å2
3----3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10387 0 81 216 10684
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 369 4.8 %
Rwork0.323 7376 -
obs-7745 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMION.TOP
X-RAY DIFFRACTION5ATP.PARAMLIGAND_NEW4.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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