[English] 日本語
Yorodumi- PDB-1ses: CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ses | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE | ||||||
Components | SERYL-tRNA SYNTHETASE | ||||||
Keywords | LIGASE / SYNTHETASE | ||||||
Function / homology | Function and homology information 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Cusack, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ses.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ses.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ses.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ses_validation.pdf.gz | 513.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ses_full_validation.pdf.gz | 541.9 KB | Display | |
Data in XML | 1ses_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1ses_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1ses ftp://data.pdbj.org/pub/pdb/validation_reports/se/1ses | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: VAL A 58 - PRO A 59 OMEGA = 210.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO A 206 / 3: CIS PROLINE - PRO A 245 / 4: CIS PROLINE - PRO A 385 / 5: CIS PROLINE - PRO B 206 / 6: CIS PROLINE - PRO B 245 / 7: CIS PROLINE - PRO B 385 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.66099, -0.48996, 0.56836), 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.) Thermus thermophilus (bacteria) / References: UniProt: P34945, serine-tRNA ligase #2: Chemical | ChemComp-AHX / | #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS REPORTED IN REFERENCE 2. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 Highest resolution: 2.5 Å / Num. obs: 36920 / % possible obs: 87 % / Num. measured all: 170878 / Rmerge(I) obs: 0.066 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→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: 2.5→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.176 / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.3 |