+Open data
-Basic information
Entry | Database: PDB / ID: 4fol | ||||||
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Title | S-formylglutathione hydrolase Variant H160I | ||||||
Components | S-formylglutathione hydrolase | ||||||
Keywords | HYDROLASE / D-type esterase / oxidation sensor motif / esterase activity activation / esterase activity inhibition | ||||||
Function / homology | Function and homology information Glutathione conjugation / S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Legler, P.M. / Millard, C.B. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2012 Title: A role for His-160 in peroxide inhibition of S. cerevisiae S-formylglutathione hydrolase: Evidence for an oxidation sensitive motif. Authors: Legler, P.M. / Leary, D.H. / Hervey, W.J. / Millard, C.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fol.cif.gz | 226.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fol.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/4fol ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4fol | HTTPS FTP |
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-Related structure data
Related structure data | 4flmC 1pv1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33952.160 Da / Num. of mol.: 4 / Mutation: H160I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YJL068C, HRE299, J1102 / Production host: Escherichia coli (E. coli) / References: UniProt: P40363, S-formylglutathione hydrolase #2: 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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.17 M ammonium acetate, 0.085 M sodium acetate trihydrate, pH 4.6, 25.5% PEG4000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→69 Å / Num. all: 82975 / Num. obs: 75437 / % possible obs: 90.9 % / Observed criterion σ(I): 3 / Redundancy: 4.11 % / Rsym value: 0.2108 / Net I/σ(I): 5.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PV1 Resolution: 2.07→61.73 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.77 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 14.702 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→61.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.123 Å / Total num. of bins used: 20
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