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- PDB-1mau: Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mau | ||||||
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Title | Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ATP and Tryptophanamide in a Pre-Transition state Conformation | ||||||
![]() | tryptophan-tRNA ligase | ||||||
![]() | LIGASE / Amino-acyl tRNA synthetase / Rossmann fold / atp binding site / pre-transition state | ||||||
Function / homology | ![]() tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter Jr., C.W. | ||||||
![]() | ![]() Title: Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. Authors: Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter, C.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 62.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m83SC ![]() 1mawC ![]() 1mb2C 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: 37225.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Non-polymers , 7 types, 127 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LTN.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LTN.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-ATP / | ||
#5: Chemical | ChemComp-LTN / | ||
#6: Chemical | ChemComp-CIT / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: microdialysis / pH: 7.5 Details: sodium citrate, magnesium chloride, sodium ATP , l-tryptophanamide, pH 7.5, MICRODIALYSIS, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 35 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 25809 / Num. obs: 23318 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.75 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1933 / Rsym value: 0.32 / % possible all: 77.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 335452 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 77.5 % / Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M83 Resolution: 2.15→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 19973 / % reflection Rfree: 10 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.209 | |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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