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Yorodumi- PDB-3fhj: Independent saturation of three TrpRS subsites generates a partia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fhj | ||||||
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Title | Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | TRANSLATION / ligand-dependent domain rearrangement / mechanistic pathway / molecular simulations / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Ligase / Nucleotide-binding / Protein biosynthesis | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Laowanapiban, P. / Kapustina, M. / Vonrhein, C. / Delarue, M. / Koehl, P. / Carter Jr., C.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2009 Title: Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Authors: Laowanapiban, P. / Kapustina, M. / Vonrhein, C. / Delarue, M. / Koehl, P. / Carter, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fhj.cif.gz | 352.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fhj.ent.gz | 287.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/3fhj ftp://data.pdbj.org/pub/pdb/validation_reports/fh/3fhj | HTTPS FTP |
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-Related structure data
Related structure data | 3fi0SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37225.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Strain: NC1500 / Gene: trpS / Plasmid: PET42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00953, tryptophan-tRNA ligase #2: Chemical | ChemComp-TRP / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-AMP / |
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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: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 315 K / pH: 6.58 Details: 2.28M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2006 |
Radiation | Monochromator: APS SERCAT 22ID BEAMLINE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 161648 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.48 % / Biso Wilson estimate: 52.66 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.65→2.85 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.22 / % possible all: 77.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FI0 Resolution: 2.65→25 Å / Occupancy max: 1 / Occupancy min: 0.33 Isotropic thermal model: We alternated the use of TLS refinement in REFMAC5 and mapping these parameters to individual isotropic B-values, which were fixed in coordinate refinements with Buster 2.0. Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 63.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å
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