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- PDB-3mey: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mey | ||||||
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Title | Crystal structure of class II aaRS homologue (Bll0957) complexed with ATP | ||||||
![]() | Bll0957 protein | ||||||
![]() | LIGASE / aminoacyl-tRNA synthetase / seryl-tRNA synthetase / zinc ion / amino acid:[carrier protein] ligase / Bll0957 | ||||||
Function / homology | ![]() : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Weygand-Durasevic, I. / Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. | ||||||
![]() | ![]() Title: Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis Authors: Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. / Weygand-Durasevic, I. #1: ![]() Title: Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition Authors: Bilokapic, S. / Maier, T. / Ahel, D. / Gruic-Sovulj, I. / Soll, D. / Weygand-Durasevic, I. / Ban, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.9 KB | Display | ![]() |
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PDB format | ![]() | 103.7 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 | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 38159.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop / pH: 4.6 Details: PEG 4000, gycerol, pH 4.6, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Mar 21, 2009 |
Radiation | Monochromator: Nova optical assembly incorporating graded multilayer optics Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20.74 Å / Num. all: 23202 / Num. obs: 23173 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7807 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.73 % / Rmerge(I) obs: 0.57 / Num. measured all: 19068 / Num. unique all: 3326 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 117.75 Å2 / Biso mean: 31.623 Å2 / Biso min: 5.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.265 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 12
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