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Yorodumi- PDB-3ls2: Crystal structure of an S-formylglutathione hydrolase from Pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ls2 | ||||||
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Title | Crystal structure of an S-formylglutathione hydrolase from Pseudoalteromonas haloplanktis TAC125 | ||||||
Components | S-formylglutathione Hydrolase | ||||||
Keywords | HYDROLASE / S-formylglutathione hydrolase / psychrophilic organism / Pseudoalteromonas haloplanktis | ||||||
Function / homology | Function and homology information S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity Similarity search - Function | ||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Alterio, V. / De Simone, G. | ||||||
Citation | Journal: Biopolymers / Year: 2010 Title: Crystal structure of an S-formylglutathione hydrolase from Pseudoalteromonas haloplanktis TAC125. Authors: Alterio, V. / Aurilia, V. / Romanelli, A. / Parracino, A. / Saviano, M. / D'Auria, S. / De Simone, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ls2.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ls2.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ls2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3ls2 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3ls2 | HTTPS FTP |
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-Related structure data
Related structure data | 1pv1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30915.732 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Strain: TAC125 / Gene: PSHAa1385 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q3IL66, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-CL / #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: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% (w/v) PEG MME 5000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 10, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 49990 / Num. obs: 49990 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4666 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PV1 Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.6 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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