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- PDB-1fyf: CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE... -

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Basic information

Entry
Database: PDB / ID: 1fyf
TitleCRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG
ComponentsTHREONYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINO ACID RECOGNITION / ZINC ION / TRNA-SYNTHETASE / ADENYLATE ANALOG / DELETION MUTANT
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
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) ...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 / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsSankaranarayanan, R. / Dock-Bregeon, A.C. / Moras, D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem.
Authors: Dock-Bregeon, A. / Sankaranarayanan, R. / Romby, P. / Caillet, J. / Springer, M. / Rees, B. / Francklyn, C.S. / Ehresmann, C. / Moras, D.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: The Structure of Threonyl-tRNA Synthetase-tRNA(Thr) Complex Enlightens its Repressor Activity and Reveals an Essential Zinc Ion in the Active Site
Authors: Sankaranarayanan, R. / Dock-Bregeon, A.C. / Romby, P. / Caillet, J. / Springer, M. / Rees, B. / Ehresmann, C. / Ehresmann, B. / Moras, D.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: Zinc Ion Mediated Amino Acid Discrimination by Threonyl-tRNA Synthetase
Authors: Sankaranarayanan, R. / Dock-Bregeon, A.C. / Rees, B. / Bovee, M. / Caillet, J. / Romby, P. / Francklyn, C.S. / Moras, D.
History
DepositionSep 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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

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Assembly

Deposited unit
A: THREONYL-TRNA SYNTHETASE
B: THREONYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4486
Polymers93,4502
Non-polymers9984
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-88 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.950, 109.520, 115.370
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 which is in the asymmetric unit.

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Components

#1: Protein THREONYL-TRNA SYNTHETASE


Mass: 46725.180 Da / Num. of mol.: 2
Fragment: CATALYTIC AND ANTICODON BINDING DOMAINS (RESIDUES 242-642)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: PEG 4000, ammonium acetate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ThrRS1reservoir
2tRNAThr1reservoir
3ammonium acetate1reservoir
4ATP1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8439 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 127385 / Num. obs: 127385 / % possible obs: 95.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.7
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.276 / Num. unique all: 7268 / % possible all: 82.9
Reflection
*PLUS
Num. measured all: 431526
Reflection shell
*PLUS
% possible obs: 82.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.65→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2345367.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5823 5 %RANDOM
Rwork0.218 ---
obs0.218 116881 88.1 %-
all-132546 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.55 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---3.34 Å20 Å2
3---4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 60 534 7127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it0.41.5
X-RAY DIFFRACTIONc_mcangle_it0.742
X-RAY DIFFRACTIONc_scbond_it0.512
X-RAY DIFFRACTIONc_scangle_it0.832.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 730 5.1 %
Rwork0.218 13637 -
obs--65.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4SSA_NEW.PARAM
X-RAY DIFFRACTION5WATER.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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