+Open data
-Basic information
Entry | Database: PDB / ID: 7br2 | ||||||
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Title | BT4096 a gut microbial diltiazem-metabolizing enzyme | ||||||
Components | Lipolytic enzyme, G-D-S-L family | ||||||
Keywords | HYDROLASE / gut microbe / diltiazem / drug metabolism / SGNH / GDSL / serine esterase | ||||||
Function / homology | : / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / Lipolytic enzyme, G-D-S-L family Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Ko, T.-P. / Chen, C.-C. / Guo, R.-T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode. Authors: Zhou, S. / Ko, T.P. / Huang, J.W. / Liu, W. / Zheng, Y. / Wu, S. / Wang, Q. / Xie, Z. / Liu, Z. / Chen, C.C. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7br2.cif.gz | 470.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7br2.ent.gz | 308.3 KB | Display | PDB format |
PDBx/mmJSON format | 7br2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7br2_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 7br2_full_validation.pdf.gz | 469 KB | Display | |
Data in XML | 7br2_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 7br2_validation.cif.gz | 102.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7br2 ftp://data.pdbj.org/pub/pdb/validation_reports/br/7br2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: -1 - 440 / Label seq-ID: 9 - 450
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-Components
#1: Protein | Mass: 51714.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_4096 / Plasmid: pET32a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A0C5 #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: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: protein: 10 mg/mL in 20 mM Tris, 500 mM NaCl, 10 mM DTT, pH 8.5 reservoir: 20% PEG 6000, 0.25 M Na-citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→25 Å / Num. obs: 91059 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 33.59 Å2 / CC1/2: 0.936 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.039 / Net I/σ(I): 25.06 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 8956 / CC1/2: 0.856 / Rpim(I) all: 0.257 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.33→24.94 Å / SU ML: 0.2566 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6236
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.02 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.39 Å
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