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Yorodumi- PDB-3ubk: Crystal structure of glutathione transferase (TARGET EFI-501770) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ubk | ||||||
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Title | Crystal structure of glutathione transferase (TARGET EFI-501770) from leptospira interrogans | ||||||
Components | Glutathione transferase | ||||||
Keywords | TRANSFERASE / GSH BINDING / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptospira interrogans serovar Lai (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Glutathione S-Transferase from Leptospira Interrogans 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ubk.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ubk.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 3ubk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ubk_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 3ubk_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 3ubk_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 3ubk_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/3ubk ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ubk | HTTPS FTP |
-Related structure data
Related structure data | 3ublC 3cbuS C: citing same article (ref.) 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: 27724.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serovar Lai (bacteria) Strain: 56601 / Gene: gst, LA_2623 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8F2Y8 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-CL / #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: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS, PH 5.5, 2M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 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: 1.94→50 Å / Num. obs: 46029 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 15.1 % / Biso Wilson estimate: 33.568 Å2 / Rsym value: 0.099 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.5 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 3CBU Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.537 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.306 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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