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- PDB-1sry: REFINED CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 1sry
TitleREFINED CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION
ComponentsSERYL-tRNA SYNTHETASE
KeywordsLIGASE(SYNTHETASE)
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine binding / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFujinaga, M. / Berthet-Colominas, C. / Cusack, S.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution.
Authors: Fujinaga, M. / Berthet-Colominas, C. / Yaremchuk, A.D. / Tukalo, M.A. / Cusack, S.
#1: 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.
#2: 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. / Haetlein, M. / Nassar, N. / Leberman, R.
History
DepositionAug 10, 1993Processing site: BNL
Revision 1.0Jan 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 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERYL-tRNA SYNTHETASE
B: SERYL-tRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)95,7582
Polymers95,7582
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.030, 127.460, 63.370
Angle α, β, γ (deg.)90.00, 108.90, 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: PHE A 262 - GLY A 263 OMEGA =144.25 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ASP A 265 - VAL A 266 OMEGA =143.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO A 385
6: LYS B 60 - ALA B 61 OMEGA =140.39 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: CIS PROLINE - PRO B 206 / 8: CIS PROLINE - PRO B 245
9: GLU B 258 - ALA B 259 OMEGA =129.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: LYS B 264 - ASP B 265 OMEGA =224.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: VAL B 266 - ARG B 267 OMEGA =210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ARG B 267 - GLY B 268 OMEGA =228.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: CIS PROLINE - PRO B 385

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.56 %
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

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 44704 / % possible obs: 97 % / Num. measured all: 234441 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: GROMOS / Classification: refinement
RefinementResolution: 2.5→10 Å / Rfactor Rwork: 0.184 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 0 190 6936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.049
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: GROMOS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_planar_d0.058
X-RAY DIFFRACTIONo_plane_restr0.05
X-RAY DIFFRACTIONo_chiral_restr0.165

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