[English] 日本語
![](img/lk-miru.gif)
- PDB-1h4s: Prolyl-tRNA synthetase from Thermus thermophilus complexed with t... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h4s | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue | |||||||||
![]() |
| |||||||||
![]() | AMINOACYL-TRNA SYNTHETASE / ATP + L-PROLINE + TRNA(PRO) AMP + PPI + L-PROLYL-TRNA(PRO) / CLASS II AMINOACYL-TRNA SYNTHETASE | |||||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yaremchuk, A. / Tukalo, M. / Cusack, S. | |||||||||
![]() | ![]() Title: A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase Authors: Yaremchuk, A. / Tukalo, M. / Grotli, M. / Cusack, S. #1: Journal: Embo J. / Year: 2000 Title: Crystal Structure of a Eukaryote/Archaeon-Like Prolyl-tRNA Synthetase and its Complex with tRNA (Pro)(Cgg) Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallisation and Preliminary X-Ray Diffraction Analysis of Thermus Thermophilus Prolyl-tRNA Synthetase Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Improved Crystals of Thermus Thermophilus Prolyl-tRNA Synthetase Complexed with Cognate tRNA Obtained by Crystallisation from Precipitate Authors: Yaremchuk, A. / Krikliviy, I. / Cusack, S. / Tukalo, M. #4: Journal: Structure / Year: 1997 Title: TRNA(Pro) Recognition by Thermus Thermophilus Prolyl-tRNA Synthetase Authors: Cusack, S. / Yaremchuk, A. / Krikliviy, I. / Tukalo, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 245.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 190.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h4qC ![]() 1h4tC ![]() 1h4vC ![]() 1hc7SC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.336459, 0.000265, -0.941698), Vector: Details | HOMODIMERIC PROLYL-TRNA SYNTHETASE AND THE RNA CHAIN | |
-
Components
-Protein / RNA chain , 2 types, 3 molecules ABT
#1: Protein | Mass: 54562.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PURIFICATION OF PROTEIN DESCRIBED IN REFERENCE 2 / Source: (natural) ![]() ![]() #2: RNA chain | | Mass: 24927.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFICATION OF TRNAPRO DESCRIBED IN REFERENCE 3 / Source: (natural) ![]() ![]() |
---|
-Non-polymers , 4 types, 40 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/P5A.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P5A.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 72 % |
---|---|
Crystal grow | pH: 7.9 / Details: SEE REFERENCE 3, pH 7.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. obs: 221758 / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.2 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 55013 / Num. measured all: 221758 |
Reflection shell | *PLUS % possible obs: 96.1 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) Resolution: 2.85→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |