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- PDB-1li7: Crystal Structure of Cysteinyl-tRNA Synthetase with Cysteine Subs... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1li7 | ||||||
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Title | Crystal Structure of Cysteinyl-tRNA Synthetase with Cysteine Substrate Bound | ||||||
![]() | CYSTEINYL-TRNA SYNTHETASE | ||||||
![]() | LIGASE / TRNA SYNTHETASE / CYSTEINE / E.COLI | ||||||
Function / homology | ![]() cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / aminoacyl-tRNA ligase activity / ligase activity / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newberry, K.J. / Hou, Y.-M. / Perona, J.J. | ||||||
![]() | ![]() Title: Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase Authors: Newberry, K.J. / Hou, Y.-M. / Perona, J.J. #1: ![]() Title: Crystallization and Preliminary Diffraction Analysis of Escherichia Coli Cysteinyl-tRNA Synthetase Authors: Newberry, K.J. / Kohn, J. / Hou, Y.-M. / Perona, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.4 KB | Display | ![]() |
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PDB format | ![]() | 122.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.9 KB | Display | ![]() |
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Full document | ![]() | 490.5 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1li5SC 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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2 | ![]()
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Unit cell |
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Details | The biological unit is a monomer with one cysteine molecule bound |
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Components
#1: Protein | Mass: 52271.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 8000, 200 MM magnesium acetate, 1MM DTT, cacodylate, 5MM ATP, 10MM cysteine. 100 MM BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: CUSTOM-MADE / Detector: CCD / Date: Sep 6, 2001 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→55 Å / Num. all: 32383 / Num. obs: 32373 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4634 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 55 Å / Rmerge(I) obs: 0.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LI5 Resolution: 2.6→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2482879.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.4565 Å2 / ksol: 0.317251 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Rfactor obs: 0.249 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.249 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.32 |