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Yorodumi- PDB-3mey: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mey | ||||||
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Title | Crystal structure of class II aaRS homologue (Bll0957) complexed with ATP | ||||||
Components | Bll0957 protein | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / seryl-tRNA synthetase / zinc ion / amino acid:[carrier protein] ligase / Bll0957 | ||||||
Function / homology | Function and homology information : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Weygand-Durasevic, I. / Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 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: Journal: Embo J. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mey.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mey.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mey_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3mey_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3mey_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3mey_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/3mey ftp://data.pdbj.org/pub/pdb/validation_reports/me/3mey | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bradyrhizobium japonicum (bacteria) / Strain: USDA110 / Gene: bll0957 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89VT8 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→20.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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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