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Yorodumi- PDB-5gvv: Crystal structure of the glycosyltransferase GlyE in Streptococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gvv | ||||||
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Title | Crystal structure of the glycosyltransferase GlyE in Streptococcus pneumoniae TIGR4 | ||||||
Components | Glycosyl transferase family 8 | ||||||
Keywords | TRANSFERASE / the glycosyltransferase / serine-rich repeat protein / Streptococcus pneumoniae | ||||||
Function / homology | : / URIDINE-5'-DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Jiang, Y.L. / Jin, H. / Zhao, R.L. / Yang, H.B. / Chen, Y. / Zhou, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Defining the enzymatic pathway for polymorphic O-glycosylation of the pneumococcal serine-rich repeat protein PsrP. Authors: Jiang, Y.L. / Jin, H. / Yang, H.B. / Zhao, R.L. / Wang, S. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gvv.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gvv.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gvv_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5gvv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5gvv_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 5gvv_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gvv ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gvv | 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
#1: Protein | Mass: 48022.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gspA_4, ERS409372_01175, ERS515225_01083 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Y1PI62 #2: Chemical | #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgCl2, 0.1 M HEPES, pH 7.5, 25% PEG 3350 |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.81 Å / Num. obs: 61392 / % possible obs: 97.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→48.81 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.81 Å
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Refine LS restraints |
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LS refinement shell |
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