+Open data
-Basic information
Entry | Database: PDB / ID: 2dxa | ||||||
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Title | Crystal structure of trans editing enzyme ProX from E.coli | ||||||
Components | Protein ybaK | ||||||
Keywords | TRANSLATION / trans-editing domain / prolyl-tRNA synthetase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Cys-tRNA(Pro) hydrolase activity / Lyases; Carbon-oxygen lyases / aminoacyl-tRNA editing activity / response to X-ray / lyase activity / translation / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of trans editing enzyme ProX from E.coli Authors: Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dxa.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dxa.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/2dxa ftp://data.pdbj.org/pub/pdb/validation_reports/dx/2dxa | HTTPS FTP |
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-Related structure data
Related structure data | 1dbxS S: Starting model for refinement |
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Similar structure data | |
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: 17824.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: cell-free protein synthesis / Plasmid: PX060110-16 / References: UniProt: P0AAR3 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3350, Tris, 10mM Cys-SA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2006 |
Radiation | Monochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→32.97 Å / Num. obs: 20627 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.031 / Net I/σ(I): 50.2 |
Reflection shell | Resolution: 1.58→1.64 Å / Rsym value: 0.096 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DBX Resolution: 1.58→32.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 863450.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.648 Å2 / ksol: 0.331002 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→32.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.68 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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