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- PDB-2x1l: Crystal structure of Mycobacterium smegmatis methionyl-tRNA synth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x1l | ||||||
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Title | Crystal structure of Mycobacterium smegmatis methionyl-tRNA synthetase in complex with methionine and adenosine | ||||||
![]() | METHIONYL-TRNA SYNTHETASE | ||||||
![]() | LIGASE / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / AMINOACYL-TRNA SYNTHETASE | ||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ingvarsson, H. / Jones, T.A. / Unge, T. | ||||||
![]() | ![]() Title: Flexibility and Communication within the Structure of the Mycobacterium Smegmatis Methionyl-tRNA Synthetase. Authors: Ingvarsson, H. / Unge, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization of Mycobacterium Smegmatis Methionyl-tRNA Synthetase in the Presence of Methionine and Adenosine. Authors: Ingvarsson, H. / Jones, T.A. / Unge, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.7 KB | Display | ![]() |
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PDB format | ![]() | 245.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 75.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x1mC ![]() 1a8hS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 59175.215 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-515 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 496 molecules ![](data/chem/img/MET.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/2HP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/2HP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M NAH2PO4, 800 MM K2HPO4, 200 MM LI2SO4, 100 MM CAPS, PH 7.0, VAPOR DIFFUSION, HANGING DROPS, TEMPERATURE 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 10, 2008 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.038 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 93306 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A8H Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.18 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 124 TO 160 AND 123 TO 158 ARE DISORDERED IN MOLECULE B AND C, RESPECTIVELY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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