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Yorodumi- PDB-5vt4: Sco GlgEI-V279S in complex with a pyrolidene-based methyl-phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vt4 | |||||||||
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Title | Sco GlgEI-V279S in complex with a pyrolidene-based methyl-phosphonate compound | |||||||||
Components | Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1 | |||||||||
Keywords | TRANSFERASE / Streptomyces coelicolor / Maltosyltransferase / transition state analogue / Alpha-1 / 4-glucan | |||||||||
Function / homology | Function and homology information starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / oligosaccharide catabolic process / hexosyltransferase activity / alpha-amylase activity Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å | |||||||||
Authors | Petit, C. / Ronning, D.R. / Lindenberger, J.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Org. Biomol. Chem. / Year: 2017 Title: Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S. Authors: Veleti, S.K. / Petit, C. / Ronning, D.R. / Sucheck, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vt4.cif.gz | 496.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vt4.ent.gz | 410.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/5vt4 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/5vt4 | HTTPS FTP |
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-Related structure data
Related structure data | 5vsjC 4cn1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 74179.133 Da / Num. of mol.: 4 / Mutation: V279S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Plasmid: pET32 / Cell (production host): BL21 / Production host: Escherichia coli (E. coli) References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring) #2: Sugar | ChemComp-9KJ / {[( #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: 3.42 Å3/Da / Density % sol: 64 % / Description: Diamond |
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Crystal grow | Temperature: 293.16 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium citrate pH 7.0 and 10 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→39.061 Å / Num. obs: 64431 / % possible obs: 99.6 % / Redundancy: 4.3 % / Net I/σ(I): 11.5 |
Reflection shell | Highest resolution: 3.2 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4cn1 Resolution: 3.205→39.061 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.205→39.061 Å
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Refine LS restraints |
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LS refinement shell |
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