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- PDB-1h4q: Prolyl-tRNA synthetase from Thermus thermophilus complexed with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h4q | ||||||
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Title | Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol | ||||||
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![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.2 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1h4sC ![]() 1h4tC ![]() 1h4vC ![]() 1hc7SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.322256, -0.002968, -0.946648), Vector: Details | HOMODIMERIC PROLYL-TRNA SYNTHETASE AND THE RNA CHAIN | |
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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) ![]() ![]() |
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-Non-polymers , 5 types, 32 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PRI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PRI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72 % |
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Crystal grow | pH: 7.9 / Details: SEE REFERENCE 3, pH 7.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 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: 3→20 Å / Num. obs: 48648 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 184299 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) Resolution: 3→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: TETRAHEDRAL CO-ORDINATION OF ZINC ATOMS TO FOUR CYSTEINES WAS RESTRAINED. SIDECHAIN ATOMS WITH OCCUPANCY ZERO HAVE POOR OR NISSING ELECTRON DENSITY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |