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Yorodumi- PDB-4nhz: Crystal structure of glutathione transferase BBTA-3750 from Brady... -
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Basic information
| Entry | Database: PDB / ID: 4nhz | ||||||
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| Title | Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290, with one glutathione bound | ||||||
Components | Putative glutathione S-transferase enzyme with thioredoxin-like domain | ||||||
Keywords | TRANSFERASE / glutathione s-transferase / Enzyme Function Initiative / EFI / structural genomics | ||||||
| Function / homology | Function and homology information | ||||||
| Biological species | Bradyrhizobium sp. (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. ...Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be PublishedTitle: Crystal Structure of Glutathione Transferase Bbta-3750 from Bradyrhizobium Sp., Target Efi-507290 Authors: Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, ...Authors: Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4nhz.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4nhz.ent.gz | 1.2 MB | Display | PDB format |
| PDBx/mmJSON format | 4nhz.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhz ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhz | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 4mf7S S: Starting model for refinement |
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| Similar structure data | |
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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: 29038.074 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: BTAI1 / ATCC BAA-1182 / Gene: BBta_3750 / Plasmid: pET / Production host: ![]() #2: Chemical | ChemComp-GSH / #3: 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: 2.27 Å3/Da / Density % sol: 45.82 % |
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| Crystal grow | pH: 8.5 Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG4000, 0.1M TRIS-HCl pH 8.5, 0.2M calcium acetate, 5 mM GSH, cryoprotectant: 20% glycerol, vapor ...Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG4000, 0.1M TRIS-HCl pH 8.5, 0.2M calcium acetate, 5 mM GSH, cryoprotectant: 20% glycerol, vapor diffusion, sitting drop, temperature 298K |
-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: Sep 18, 2013 / Details: MIRRORS |
| Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
| Reflection | Resolution: 1.9→50 Å / Num. obs: 309970 / % possible obs: 97.2 % / Observed criterion σ(I): -5 / Redundancy: 2 % / Rsym value: 0.047 / Net I/σ(I): 8.8 |
| Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / % possible all: 95.1 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4MF7 Resolution: 1.901→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.381 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 31.684 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.901→50 Å
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| Refine LS restraints |
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Bradyrhizobium sp. (bacteria)
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