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- PDB-1set: CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNT... -

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Entry
Database: PDB / ID: 1set
TitleCRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE
ComponentsSERYL-tRNA SYNTHETASE
KeywordsLIGASE / SYNTHETASE
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / serine binding / tRNA binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsCusack, S. / Belrhali, H.
Citation
Journal: Science / Year: 1994
Title: Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.
Authors: Belrhali, H. / Yaremchuk, A. / Tukalo, M. / Larsen, K. / Berthet-Colominas, C. / Leberman, R. / Beijer, B. / Sproat, B. / Als-Nielsen, J. / Grubel, G. / Legrand, J.-F. / Lehmann, M. / Cusack, S.
#1: Journal: Science / Year: 1994
Title: The 2.9 Angstroms Crystal Structure of T. Thermophilus Seryl-tRNA Synthetase Complexed with tRNA-Ser
Authors: Biou, V. / Yaremchuk, A. / Tukalo, M. / Cusack, S.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Crystal Structure of the Seryl-tRNA Synthetase from Thermus Thermophilus at 2.5 Angstroms Resolution
Authors: Fujinaga, M. / Berthet-Colominas, C. / Yaremchuk, A.D. / Tukalo, M.A. / Cusack, S.
#3: Journal: FEBS Lett. / Year: 1993
Title: Crystallization of the Seryl-tRNA Synthetase: TRNA-Ser Complex of Escherichia Coli
Authors: Price, S. / Cusack, S. / Borel, F. / Berthet-Colominas, C. / Leberman, R.
#4: Journal: FEBS Lett. / Year: 1992
Title: A New Crystal Form of the Complex between Seryl-tRNA Synthetase and tRNA-Ser from Thermus Thermophilus that Diffracts to 2.8 Angstroms Resolution
Authors: Yaremchuk, A.D. / Tukalo, M.A. / Krikliviy, I. / Malchenko, N. / Biou, V. / Berthet-Colominas, C. / Cusack, S.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of the Seryl-tRNA Synthetase-tRNA-Ser Complex from Thermus Thermophilus
Authors: Yaremchuk, A.D. / Tukalo, M.A. / Krikliviy, I. / Mel'Nik, V.N. / Berthet-Colominas, C. / Cusack, S. / Leberman, R.
#6: Journal: Nucleic Acids Res. / Year: 1991
Title: Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl-tRNA Synthetases
Authors: Cusack, S. / Hartlein, M. / Leberman, R.
#7: Journal: Nature / Year: 1990
Title: Seryl-tRNA Synthetase from Escherichia Coli at 2.5 Angstroms Resolution: A Second Class of Synthetase Structure
Authors: Cusack, S. / Berthet-Colominas, C. / Hartlein, M. / Nassar, N. / Leberman, R.
#8: Journal: J.Mol.Biol. / Year: 1990
Title: Crystals of Seryl-tRNA Synthetase from Thermus Thermophilus. Preliminary Crystallographic Data
Authors: Garber, M.B. / Yaremchuk, A.D. / Tukalo, M.A. / Egorova, S.P. / Berthet-Colominas, C. / Leberman, R.
History
DepositionFeb 21, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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: SERYL-tRNA SYNTHETASE
B: SERYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6244
Polymers95,7582
Non-polymers8672
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-20 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 126.300, 62.900
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 206 / 2: CIS PROLINE - PRO A 245 / 3: CIS PROLINE - PRO A 385 / 4: CIS PROLINE - PRO B 206 / 5: CIS PROLINE - PRO B 245 / 6: CIS PROLINE - PRO B 385
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.65768, -0.49078, 0.57148), (-0.49222, -0.85427, -0.16716), (0.57023, -0.17136, -0.80341)
Vector: -13.96815, 32.38737, 68.35971)
DetailsTHE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATION TO GO FROM MONOMER 1 TO MONOMER 2 IS GIVEN ON *MTRIX* RECORDS BELOW. IT WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. IT IS BASED ON SIMULTANEOUS SUPERPOSITION OF THE C-ALPHAS OF RESIDUES 100 - 258 AND 270 - 419.

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Components

#1: Protein SERYL-tRNA SYNTHETASE


Mass: 47878.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P34945, serine-tRNA ligase
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


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


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS REPORTED IN REFERENCE 2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 %satammonium sulfate1drop
350 mMMES1drop
45 mMdithiothreitol1drop
510 mM1dropMgCl2
61 mM1dropNaN3
71 %(v/v)MPD1drop
830-35 %satammonium sulfate1reservoir
98 %MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 38589 / % possible obs: 91 % / Num. measured all: 217462 / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.55→20 Å / σ(F): 2
Details: RESIDUES WITH NO ELECTRON DENSITY OR B GREATER THAN 90 HAVE OCCUPANCY 0.0.
RfactorNum. reflection
Rwork0.185 -
obs0.185 38589
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 58 170 6974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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