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- PDB-1ser: THE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA... -

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Entry
Database: PDB / ID: 1ser
TitleTHE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA SER
Components
  • PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))
  • TRNASER
KeywordsLIGASE/RNA / PROTEIN-T-RNA COMPLEX / LIGASE-RNA COMPLEX
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
RNA / RNA (> 10) / Serine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsBiou, S. / Cusack, V. / Yaremchuk, A. / Tukalo, M.
Citation
Journal: Science / Year: 1994
Title: The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser).
Authors: Biou, V. / Yaremchuk, A. / Tukalo, M. / Cusack, S.
#1: Journal: Science / Year: 1994
Title: Crystal Structures at 2.5 Angstroms Resolution of Seryl-tRNA Synthetase Complexed with Two Different Analogues of Seryl-Adenylate
Authors: Belrhali, H. / Yaremchuk, A.D. / Tukalo, M.A. / Larsen, K. / Berthet-Colominas, C. / Leberman, R. / Beijer, B. / Sproat, B. / Als-Nielsen, J. / Grubel, G. / Legrand, J.-F. / Lehmann, 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, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TRNASER
A: PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))
B: PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))


Theoretical massNumber of molelcules
Total (without water)126,1453
Polymers126,1453
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.500, 128.900, 121.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 706 / 5: CIS PROLINE - PRO B 745 / 6: CIS PROLINE - PRO B 885
7: TRNA RIBOSES G 7, G 9, G 18, G 19, C 20, D 20A, G 20B, C 48, A 58 AND U 60 HAVE BEEN CONSTRAINED TO 2'ENDO PUCKER. ALL OTHERS ARE 3' ENDO.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.63067, -0.18036, -0.7548), (-0.17168, -0.91609, 0.36235), (-0.75683, 0.35811, 0.54679)
Vector: 232.72008, 88.27364, 93.039)
DetailsTHE MATRIX PRESENTED IN *MTRIX* RECORDS BELOW IS THE ORTHOGONAL TRANSFORMATION TO GO FROM MONOMER 1 TO MONOMER 2 OF THE SYNTHETASE BASED ON SIMULTANEOUS SUPERPOSITION OF C-ALPHAS OF RESIDUES A 100 - 258 ON B 600 - 758 AND A 270 - 419 ON B 770 - 919.

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Components

#1: RNA chain TRNASER


Mass: 30387.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: Protein PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))


Mass: 47878.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P34945
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE IS REPORTED IN REFERENCE 2 (SEE ABOVE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
22.5 mMmagnesium chloride1drop
1ammonium sulfate1dropor sodium citrate

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 41675 / % possible obs: 95 % / Rmerge(I) obs: 0.067

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.9→10 Å / σ(F): 0.5
Details: SERYL-TRNA SYNTHETASE IS A CLASS 2 AMINOACYL-TRNA SYNTHETASE. SERYL-TRNA SYNTHETASE FROM T. THERMOPHILUS IS AN HOMO-DIMER WITH 421 RESIDUES PER SUBUNIT. MONOMER 1 (IDENTIFIER SST1) HAS ...Details: SERYL-TRNA SYNTHETASE IS A CLASS 2 AMINOACYL-TRNA SYNTHETASE. SERYL-TRNA SYNTHETASE FROM T. THERMOPHILUS IS AN HOMO-DIMER WITH 421 RESIDUES PER SUBUNIT. MONOMER 1 (IDENTIFIER SST1) HAS RESIDUES 1 - 421. RESIDUES 39 - 87 ARE ABSENT IN THE ELECTRON DENSITY OF THIS STRUCTURE DUE TO DISORDER. RESIDUES 261 - 264 ARE ABSENT FROM THE ELECTRON DENSITY BUT ARE INCLUDED IN THE MODEL WITZ ZERO OCCUPANCY MONOMER 2 (IDENTIFIER SST2) HAS RESIDUES 501 - 921. THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B (MONOMER 2) WHEN APPLIED TO CHAIN A (MONOMER 1). THERE IS ONLY ONE TRNA MOLECULE (IDENTIFIER TRN1) COMPLEXED WITH THE DIMERIC SYNTHETASE IN THIS STRUCTURE. THIS IS DESIGNATED TRNASER2 WITH ANTICODON GGA AND IT CONTAINS 94 NUCLEOTIDES. NUCLEOTIDES ARE NUMBERED 1 - 16, 18 - 20, 20A, 20B, 21 - 47, 47A - 47Q, 48 - 76. NUCLEOTIDES 45 - 47Q CONSTITUTE THE LONG VARIABLE ARM OF THE TRNA. THE SEQUENCE IS (APART FROM MODIFIED BASES): GUA 001 GUA 002 ADE 003 GUA 004 ADE 005 GUA 006 GUA 007 URI 008 GUA 009 CYT 010 CYT 011 CYT 012 GUA 013 ADE 014 GUA 015 URI 016 GUA 018 GUA 019 CYT 020 DHU 20A GUA 20B ADE 021 ADE 022 GUA 023 GUA 024 GUA 025 ADE 026 CYT 027 ADE 028 CYT 029 GUA 030 ADE 031 CYT 032 URI 033 GUA 034 GUA 035 ADE 036 ADE 037 ADE 038 URI 039 CYT 040 GUA 041 URI 042 GUA 043 URI 044 ADE 045 GUA 046 GUA 047 GUA 47A GUA 47B GUA 47C GUA 47D CYT 47E URI 47F URI 47G ADE 47H ADE 47I ADE 47J CYT 47K CYT 47L URI 47M CYT 47N CYT 47O CYT 47P URI 47Q CYT 048 GUA 049 CYT 050 GUA 051 GUA 052 GUA 053 THY 054 PSU 055 CYT 056 GUA 057 ADE 058 ADE 059 URI 060 CYT 061 CYT 062 CYT 063 GUA 064 CYT 065 CYT 066 CYT 067 URI 068 CYT 069 URI 070 CYT 071 CYT 072 GUA 073 CYT 074 CYT 075 ADE 076 IN THE CRYSTAL STRUCTURE SIGNIFICANT PARTS OF THE TRNA ARE MISSING FROM THE ELECTRON DENSITY DUE TO DISORDER. THEREFORE COORDINATES ARE NOT GIVEN FOR NUCLEOTIDES 1 - 3, 26 - 41, 47E - 47J, 72 - 76. TRNA RIBOSES G 7, G 9, G 18, G 19, C 20, D 20A, G 20B, C 48, A 58 AND U 60 HAVE BEEN CONSTRAINED TO 2'ENDO PUCKER. ALL OTHERS ARE 3' ENDO.
RfactorNum. reflection% reflection
Rwork0.194 --
obs0.194 39713 92.9 %
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6355 1381 0 44 7780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.3
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
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / σ(F): 0.5 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.3

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