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Yorodumi- PDB-6xpm: Crystal Structure of Sialate O-acetylesterase from Bacteroides vu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xpm | ||||||
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Title | Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature | ||||||
Components | Lysophospholipase L1 | ||||||
Keywords | HYDROLASE / Sialate O-acetylesterase / alpha-beta fold / microfluidics / Structural Genomics / Midwest Center for Structural Genomics / PSI-Biology / MCSG | ||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / Hydrolases; Acting on ester bonds / metal ion binding / SGNH/GDSL hydrolase family protein / Sialate O-acetylesterase Function and homology information | ||||||
Biological species | Bacteroides vulgatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kim, Y. / Johnson, J. / Welk, L. / Endres, M. / Levens, A. / Sherrell, D.A. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature Authors: Kim, Y. / Johnson, J. / Welk, L. / Endres, M. / Levens, A. / Sherrell, D.A. / Babnigg, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xpm.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xpm.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/6xpm ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xpm | HTTPS FTP |
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-Related structure data
Related structure data | 6njcS 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: 22970.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus (bacteria) Gene: DW857_02595, DW869_04095, DWX04_04065, DWZ06_04430, DXA04_10705, EAJ12_11850, ERS852457_01148, ERS852509_00617, ERS852556_01195, SAMN04487923_100221 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold References: UniProt: A0A174J845, UniProt: A6L7S9*PLUS, Hydrolases |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.85 % |
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Crystal grow | Temperature: 295 K / Method: microfluidic / pH: 4.5 Details: 0.2 M lithium sulfate, 0.1 M acetate, pH 4.5, 2.5 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 4, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 14414 / % possible obs: 97.8 % / Redundancy: 22.4 % / Biso Wilson estimate: 54.72 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.158 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 620 / CC1/2: 0.461 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6NJC Resolution: 2.3→33.59 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8964 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 62.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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