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Yorodumi- PDB-3mf2: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mf2 | ||||||
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Title | Crystal structure of class II aaRS homologue (Bll0957) complexed with AMP | ||||||
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 / SYNCHROTRON / SAD / Resolution: 2.15 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 | 3mf2.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mf2.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 3mf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mf2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3mf2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3mf2_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 3mf2_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/3mf2 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mf2 | 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: 2.11 Å3/Da / Density % sol: 41.59 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.282 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 278833 / Rmerge(I) obs: 0.055 / D res high: 2.15 Å / D res low: 46.74 Å / Num. obs: 35847 / % possible obs: 99.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.15→46.74 Å / Num. all: 35915 / Num. obs: 35847 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.182 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.15→2.28 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 40479 / Num. unique obs: 10638 / % possible all: 96.8 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→29.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 135.85 Å2 / Biso mean: 41.383 Å2 / Biso min: 18.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.217 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 18
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