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Yorodumi- PDB-3e26: Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+26 | ||||||
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Title | Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate synthase | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | TRANSFERASE / glucosyltransferase / mycobacterial / GT81 UDP-glucose / 3-phosphoglycerate | ||||||
Function / homology | Function and homology information glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / glycosyltransferase activity / magnesium ion binding / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Pereira, P.J.B. / Empadinhas, N. / Costa, M.S. / Macedo-Ribeiro, S. | ||||||
Citation | Journal: Plos One / Year: 2008 Title: Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis Authors: Pereira, P.J.B. / Empadinhas, N. / Albuquerque, L. / Sa-Moura, B. / da Costa, M.S. / Macedo-Ribeiro, S. #1: Journal: Fems Microbiol.Lett. / Year: 2008 Title: Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase Authors: Empadinhas, N. / Albuquerque, L. / Mendes, V. / Macedo-Ribeiro, S. / da Costa, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e26.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e26.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3e26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e26_validation.pdf.gz | 414.1 KB | Display | wwPDB validaton report |
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Full document | 3e26_full_validation.pdf.gz | 418 KB | Display | |
Data in XML | 3e26_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3e26_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e26 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e26 | 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: 35938.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1246, Rv1208 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: 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: 4.36 Å3/Da / Density % sol: 71.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris pH 8.0, 0.5% polyethyleneglycol monomethyl ether 5000, 0.65M Na-K phosphate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→78.3 Å / Num. all: 21338 / Num. obs: 21338 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 53.97 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.07 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3117 / Rsym value: 0.386 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rubrobacter xylanophilus mannosyl-3-phosphoglycerate synthase (Sa-Moura et al., Acta Cryst. (2008). F64, 760-763) Resolution: 2.5→70.374 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 24.29 / 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 / Bsol: 65.064 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.33 Å2 / Biso mean: 65.546 Å2 / Biso min: 42.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→70.374 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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