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Yorodumi- PDB-4ipl: The crystal structure of 6-phospho-beta-glucosidase BglA-2 from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ipl | ||||||
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Title | The crystal structure of 6-phospho-beta-glucosidase BglA-2 from Streptococcus pneumoniae | ||||||
Components | 6-phospho-beta-glucosidase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å | ||||||
Authors | Yu, W.L. / Jiang, Y.L. / Andreas, P. / Cheng, W. / Bai, X.H. / Ren, Y.M. / Thompsonn, J. / Zhou, C.Z. / Chen, Y.X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural insights into the substrate specificity of a 6-phospho-&[beta]-glucosidase BglA-2 from Streptococcus pneumoniae TIGR4 Authors: Yu, W.L. / Jiang, Y.L. / Pikis, A. / Cheng, W. / Bai, X.H. / Ren, Y.M. / Thompson, J. / Zhou, C.Z. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ipl.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ipl.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ipl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ipl_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 4ipl_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 4ipl_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 4ipl_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/4ipl ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4ipl | HTTPS FTP |
-Related structure data
-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: 56225.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: bglA-2, SP_0578 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q97S37, UniProt: A0A0H2UP35*PLUS, 6-phospho-beta-glucosidase #2: Chemical | ChemComp-GOL / | #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: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15% polyethylene glycol 5000MME, 0.1 M sodium citrate tribasic dehydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 73344 / Num. obs: 72464 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2→2.11 Å / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→31.672 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 25.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.1 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.004→31.672 Å
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Refine LS restraints |
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LS refinement shell |
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