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Yorodumi- PDB-4nhw: Crystal structure of glutathione transferase SMc00097 from Sinorh... -
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-Basic information
Entry | Database: PDB / ID: 4nhw | ||||||
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Title | Crystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275, with one glutathione bound per one protein subunit | ||||||
Components | Glutathione S-transferase | ||||||
Keywords | TRANSFERASE / glutathione S-transferase / Enzyme Function Initiative / EFI / structural genomics | ||||||
Function / homology | Function and homology information Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nhw.cif.gz | 356.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nhw.ent.gz | 291.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nhw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4nhw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4nhw_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 4nhw_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhw ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhw | HTTPS FTP |
-Related structure data
Related structure data | 3lszS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 26926.604 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: gst2, SM2011_c00097 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M4MQ92, glutathione transferase #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: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | pH: 6.5 Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, vapor diffusion, ...Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, 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: Oct 17, 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: 2→50 Å / Num. obs: 62866 / % possible obs: 96.1 % / Observed criterion σ(I): -5 / Redundancy: 2 % / Rsym value: 0.047 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.1 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LSZ Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.136 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.183 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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