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- PDB-4dej: Crystal structure of glutathione transferase-like protein IL0419 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dej | ||||||
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Title | Crystal structure of glutathione transferase-like protein IL0419 (Target EFI-501089) from Idiomarina loihiensis L2TR | ||||||
![]() | Glutathione S-transferase related protein | ||||||
![]() | TRANSFERASE / TRANSFERASE-LIKE PROTEIN / TRANSCRIPTION REGULATION / Structural Genomics | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
![]() | ![]() Title: Crystal Structure of Glutathione S-Transferase-Like Protein Il0419 from Idiomarina Loihiensis Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 485.2 KB | Display | ![]() |
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PDB format | ![]() | 400.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 545.6 KB | Display | ![]() |
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Full document | ![]() | 572.8 KB | Display | |
Data in XML | ![]() | 77 KB | Display | |
Data in CIF | ![]() | 102.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yy7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 27010.842 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M AMMONIUM SULFATE, 0.1M HEPES-NA, 30% PEG8000', pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→70 Å / Num. obs: 87401 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 6.7 % / Biso Wilson estimate: 96.503 Å2 / Rsym value: 0.08 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.7 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YY7 Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.436 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.323 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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