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- PDB-1p7p: Methionyl-tRNA synthetase from Escherichia coli complexed with me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p7p | ||||||
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Title | Methionyl-tRNA synthetase from Escherichia coli complexed with methionine phosphonate | ||||||
![]() | Methionyl-tRNA synthetase | ||||||
![]() | LIGASE / Rossmann fold | ||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crepin, T. / Schmitt, E. / Mechulam, Y. / Sampson, P.B. / Vaughan, M.D. / Honek, J.F. / Blanquet, S. | ||||||
![]() | ![]() Title: Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. Authors: Crepin, T. / Schmitt, E. / Mechulam, Y. / Sampson, P.B. / Vaughan, M.D. / Honek, J.F. / Blanquet, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.6 KB | Display | ![]() |
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PDB format | ![]() | 100.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pfuC ![]() 1pfvC ![]() 1pfwC ![]() 1pfyC ![]() 1pg0C ![]() 1pg2C ![]() 1qqtS 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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Unit cell |
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Components
#1: Protein | Mass: 62958.102 Da / Num. of mol.: 1 / Fragment: Residues 4-548 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MPH / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.41 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion / pH: 7 Details: ammonium citrate, potassium phosphate, pH 7, VAPOR DIFFUSION, temperature 280K |
Crystal grow | *PLUS Method: unknown / Details: Mechulam, Y., (1999) J. Mol. Biol., 294, 1287. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. all: 51316 / Num. obs: 51316 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 16.35 Å2 / Rsym value: 0.059 |
Reflection shell | Resolution: 1.78→1.87 Å / Redundancy: 2.1 % / Num. unique all: 7523 / Rsym value: 0.28 / % possible all: 93.4 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 52574 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QQT Resolution: 1.8→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å /
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.005 |