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- PDB-1obh: LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1obh | ||||||
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Title | LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND EDITING SITE | ||||||
![]() | LEUCYL-TRNA SYNTHETASE | ||||||
![]() | SYNTHETASE / AMINOACYL-TRNA SYNTHETASE / CLASS I AMINOACYL-TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) -> AMP + PPI L- LEUCYL-TRNA(LEU) | ||||||
Function / homology | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. / Yaremchuk, A. / Tukalo, M. | ||||||
![]() | ![]() Title: Structural and Mechanistic Basis of Pre- and Posttransfer Editing by Leucyl-tRNA Synthetase Authors: Lincecum, T. / Tukalo, M. / Yaremchuk, A. / Mursinna, R. / Williams, A. / Sproat, B. / Van Den Eynde, W. / Link, A. / Van Calenbergh, S. / Grotli, M. / Martinis, S. / Cusack, S. #1: ![]() Title: The 2A Structure of Leucyl-tRNA Synthetase and its Complex with a Leucyl-Adenylate Analogue Authors: Cusack, S. / Yaremchuk, A. / Tukalo, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary Crystallographic Analysis of Thermus Thermophilus Leucyl-tRNA Synthetase and its Complexes with Leucine and a Non-Hydrolysable Leucyl-Adenylate Analogue Authors: Yaremchuk, A. / Cusack, S. / Gudzera, O. / Grotli, M. / Tukalo, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.9 KB | Display | ![]() |
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PDB format | ![]() | 136.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1obcC ![]() 1h3nS S: Starting model for refinement C: citing same article ( |
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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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 101170.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ENZYME CONTAINS 878 RESIDUES / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 208 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/NVA.gif)
![](data/chem/img/LMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/NVA.gif)
![](data/chem/img/LMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HG / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE ...Details: PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5. SEE REFERENCE 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: used microseeding, Yaremchuk, A., (2000) Acta Crystallogr., 56, 667. PH range low: 6.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CCD / Detector: CCD / Date: Jul 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 68288 / % possible obs: 98.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 85.8 |
Reflection shell | *PLUS % possible obs: 85.8 % / Rmerge(I) obs: 0.388 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H3N Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SIDE-CHAINS ATOMS WITH NO ELECTRON DENSITY HAVE ZERO OCCUPANCY.THE ZN1 DOMAIN, RESIDUES 154-189, ARE DISORDERED IN THIS CRYSTAL FORM. PARTS OF THE ZN2 DOMAIN, RESIDUES 440-443, 466-470, 486- ...Details: SIDE-CHAINS ATOMS WITH NO ELECTRON DENSITY HAVE ZERO OCCUPANCY.THE ZN1 DOMAIN, RESIDUES 154-189, ARE DISORDERED IN THIS CRYSTAL FORM. PARTS OF THE ZN2 DOMAIN, RESIDUES 440-443, 466-470, 486-492 ARE DISORDERED IN THIS CRYSTAL FORM. THE C-TERMINAL DOMAIN, RESIDUES 815-878, ARE DISORDERED IN THE CRYSTAL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1749 Å2 / ksol: 0.360808 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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