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Yorodumi- PDB-4y7f: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y7f | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and 3-(phosphonooxy)propanoic acid (PPA) - GpgS Mn2+ UDP-Glc PPA | ||||||
Components | Glucosyl-3-phosphoglycerate synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.231 Å | ||||||
Authors | Albesa-Jove, D. / Rodrigo-Unzueta, A. / Cifuente, J.O. / Urresti, S. / Comino, N. / Sancho-Vaello, E. / Guerin, M.E. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase. Authors: Albesa-Jove, D. / Mendoza, F. / Rodrigo-Unzueta, A. / Gomollon-Bel, F. / Cifuente, J.O. / Urresti, S. / Comino, N. / Gomez, H. / Romero-Garcia, J. / Lluch, J.M. / Sancho-Vaello, E. / ...Authors: Albesa-Jove, D. / Mendoza, F. / Rodrigo-Unzueta, A. / Gomollon-Bel, F. / Cifuente, J.O. / Urresti, S. / Comino, N. / Gomez, H. / Romero-Garcia, J. / Lluch, J.M. / Sancho-Vaello, E. / Biarnes, X. / Planas, A. / Merino, P. / Masgrau, L. / Guerin, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y7f.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y7f.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 4y7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y7f_validation.pdf.gz | 808.8 KB | Display | wwPDB validaton report |
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Full document | 4y7f_full_validation.pdf.gz | 810.6 KB | Display | |
Data in XML | 4y7f_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 4y7f_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/4y7f ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7f | HTTPS FTP |
-Related structure data
Related structure data | 4y6nC 4y6uC 4y7gC 4y9xC 4decS 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 A
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: gpgS, Rv1208 / Plasmid: pET29a::GSGA-Rv1208 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase |
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-Non-polymers , 6 types, 37 molecules
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-48X / |
#4: Chemical | ChemComp-UPG / |
#5: Chemical | ChemComp-SO4 / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14% PEG 8,000, 0.3-0.5 M Li sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2013 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.23→69.25 Å / Num. obs: 9590 / % possible obs: 99.66 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.97 |
Reflection shell | Resolution: 3.23→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.5 / % possible all: 99.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DEC Resolution: 3.231→69.25 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 23.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.231→69.25 Å
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Refine LS restraints |
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LS refinement shell |
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