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Yorodumi- PDB-4ibp: Crystal structure of a glutathione transferase family member from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ibp | ||||||
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Title | Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target EFI-900011, with bound glutathione | ||||||
Components | Glutathione S-transferase-like protein YibF | ||||||
Keywords | TRANSFERASE / GST / glutathione S-transferase / enzyme function initiative / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase activity / glutathione metabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target IFI-900011, with bound glutathione Authors: Vetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Gerlt, J.A. / 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 | 4ibp.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ibp.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ibp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ibp_validation.pdf.gz | 750.7 KB | Display | wwPDB validaton report |
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Full document | 4ibp_full_validation.pdf.gz | 752.4 KB | Display | |
Data in XML | 4ibp_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4ibp_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibp ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibp | HTTPS FTP |
-Related structure data
Related structure data | 3touS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24413.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: yibF, PFL_5710 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K4R5 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GSH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.1 M Bis-Tris Propane:HCl pH 7.0, 1.8 M Magnesium Sulfate); Cryoprotection (20 mM Bis-Tris Propane:HCl pH 7.0, 2.2 M Magnesium Sulfate ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.1 M Bis-Tris Propane:HCl pH 7.0, 1.8 M Magnesium Sulfate); Cryoprotection (20 mM Bis-Tris Propane:HCl pH 7.0, 2.2 M Magnesium Sulfate + 2 mM reduce glutathione), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2012 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38.66 Å / Num. all: 30206 / Num. obs: 30206 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 40.46 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4410 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TOU Resolution: 1.8→38.659 Å / Occupancy max: 1 / Occupancy min: 0.9 / FOM work R set: 0.7046 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 34.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.44 Å2 / Biso mean: 50.0895 Å2 / Biso min: 30.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→38.659 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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