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Yorodumi- PDB-4mzw: CRYSTAL STRUCTURE OF NU-CLASS GLUTATHIONE TRANSFERASE YGHU FROM S... -
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-Basic information
Entry | Database: PDB / ID: 4mzw | ||||||
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Title | CRYSTAL STRUCTURE OF NU-CLASS GLUTATHIONE TRANSFERASE YGHU FROM Streptococcus sanguinis SK36, COMPLEX WITH GLUTATHIONE DISULFIDE, TARGET EFI-507286 | ||||||
Components | Glutathione S-Transferase | ||||||
Keywords | TRANSFERASE / GLUTATHIONE S-TRANSFERASE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / GLUTATHIONE DISULFIDE | ||||||
Function / homology | Function and homology information Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptococcus sanguinis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 S-Transferase Yghu (Target Efi-507286) 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 | 4mzw.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mzw.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mzw_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4mzw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4mzw_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 4mzw_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/4mzw ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mzw | HTTPS FTP |
-Related structure data
Related structure data | 3c8eS 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: 31711.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: SSA_1418 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3CNR0 #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | pH: 7 Details: 1.1M Malonic Acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic Acid, 0.18M DL-Malic Acid, 0.24M Sodium Acetate, 0.3M Sodium Formate, 0.096M Ammonium Tartrate Dibasic, pH 7.0, 5MM GSH, ...Details: 1.1M Malonic Acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic Acid, 0.18M DL-Malic Acid, 0.24M Sodium Acetate, 0.3M Sodium Formate, 0.096M Ammonium Tartrate Dibasic, pH 7.0, 5MM GSH, PROTEIN IN 10MM HEPES, PH 7.5, 150MM SODIUM CHLORIDE, 5% GLYCEROL, 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: 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: 1.95→50 Å / Num. obs: 47570 / % possible obs: 99.3 % / Observed criterion σ(I): -5 / Redundancy: 13.2 % / Rsym value: 0.075 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C8E Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.308 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / 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: 40.471 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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