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Yorodumi- PDB-8hwp: Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hwp | ||||||
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Title | Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 S12A in Complex with Butyrate | ||||||
Components | GDSL-family esterase | ||||||
Keywords | HYDROLASE / GDSL esterase / butyrate / complex | ||||||
Function / homology | GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / butanoic acid / GDSL-family esterase Function and homology information | ||||||
Biological species | Photobacterium sp. J15 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Rahman, N.N.A. / Leow, T.C. / Jonet, M.A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 in Complex with Butyrate Authors: Rahman, N.N.A. / Leow, T.C. / Jonet, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hwp.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hwp.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/8hwp ftp://data.pdbj.org/pub/pdb/validation_reports/hw/8hwp | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35643.965 Da / Num. of mol.: 1 / Mutation: S12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium sp. J15 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0PV22 |
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#2: Chemical | ChemComp-BUA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate as salt, 30% (w/v) polyethylene glycol 4,000 as precipitant in 0.1 M sodium acetate trihydrate buffer at pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Apr 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. obs: 117000 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 16.78 Å2 / CC1/2: 0.79 / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.73→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.339 / Num. unique obs: 39377 / CC1/2: 0.79 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→50 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→50 Å
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Refine LS restraints |
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LS refinement shell |
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