[English] 日本語
![](img/lk-miru.gif)
- PDB-1set: CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNT... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1set | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE | ||||||
![]() | SERYL-tRNA SYNTHETASE | ||||||
![]() | LIGASE / SYNTHETASE | ||||||
Function / homology | ![]() selenocysteine biosynthetic process / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / serine binding / tRNA binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Cusack, S. / Belrhali, H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() Title: Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl-tRNA Synthetases Authors: Cusack, S. / Hartlein, M. / Leberman, R. #7: ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 181.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 529.9 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: 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), Vector: Details | THE 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. | |
-
Components
#1: Protein | Mass: 47878.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS REPORTED IN REFERENCE 2. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density 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
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 38589 / % possible obs: 91 % / Num. measured all: 217462 / Rmerge(I) obs: 0.075 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.55→20 Å / σ(F): 2 Details: RESIDUES WITH NO ELECTRON DENSITY OR B GREATER THAN 90 HAVE OCCUPANCY 0.0.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |