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Yorodumi- PDB-5t9c: Crystal structure of B. subtilis 168 GlpQ in complex with glycero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t9c | |||||||||
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Title | Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour soak) | |||||||||
Components | Glycerophosphoryl diester phosphodiesterase | |||||||||
Keywords | HYDROLASE / metal binding protein | |||||||||
Function / homology | Function and homology information glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / glycerol metabolic process / lipid metabolic process / cell wall organization / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Li, F.K.K. / Strynadka, N.C.J. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component. Authors: Myers, C.L. / Li, F.K. / Koo, B.M. / El-Halfawy, O.M. / French, S. / Gross, C.A. / Strynadka, N.C. / Brown, E.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t9c.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t9c.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 5t9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t9c_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 5t9c_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 5t9c_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5t9c_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/5t9c ftp://data.pdbj.org/pub/pdb/validation_reports/t9/5t9c | HTTPS FTP |
-Related structure data
Related structure data | 5t91C 5t9bC 4r70S C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 30202.641 Da / Num. of mol.: 1 / Fragment: UNP residues 27-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: glpQ, ybeD, BSU02130 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P37965, glycerophosphodiester phosphodiesterase |
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-Non-polymers , 5 types, 169 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-G3P / |
#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM bicine, pH 8.5, 25% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03322 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 9, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→48.49 Å / Num. obs: 40774 / % possible obs: 99.67 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.698 / % possible all: 98.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4R70 Resolution: 1.48→48.49 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.48→48.49 Å
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LS refinement shell | Resolution: 1.48→1.53 Å
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