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Yorodumi- PDB-3m5w: Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m5w | ||||||
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Title | Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / alpha-beta structure / CSGID / Aminoacyl-tRNA synthetase / ATP-binding / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published / Year: 2010 Title: Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni Authors: Kim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m5w.cif.gz | 263.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m5w.ent.gz | 224.7 KB | Display | PDB format |
PDBx/mmJSON format | 3m5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m5w_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
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Full document | 3m5w_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 3m5w_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 3m5w_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/3m5w ftp://data.pdbj.org/pub/pdb/validation_reports/m5/3m5w | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36873.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0388, trpS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PIB4, tryptophan-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 / Details: mirrors |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. all: 29722 / Num. obs: 29722 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.131 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1438 / Rsym value: 0.707 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.32→47.811 Å / SU ML: 0.33 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.821 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→47.811 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | S21: -0.0216 Å ° / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain B |