[English] 日本語
Yorodumi- PDB-5jsx: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jsx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+ and uridine-diphosphate-glucose (UDP-Glc) | ||||||
Components | glucosyl-3-phosphoglycerate synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Mycobacterium tuberculosis H37Ra (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Albesa-Jove, D. / Sancho-Vaello, E. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Guerin, M.E. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS. Authors: Albesa-Jove, D. / Romero-Garcia, J. / Sancho-Vaello, E. / Contreras, F.X. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Biarnes, X. / Planas, A. / Guerin, M.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jsx.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jsx.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/5jsx ftp://data.pdbj.org/pub/pdb/validation_reports/js/5jsx | HTTPS FTP |
---|
-Related structure data
Related structure data | 5jqxC 5jt0C 5jucC 5judC 4y6nS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria) Gene: MRA_1217 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U1Q6 |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-UPG / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.66 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→69.85 Å / Num. obs: 14927 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 85.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06335 / Net I/σ(I): 14.52 |
Reflection shell | Resolution: 2.81→2.91 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.4811 / Mean I/σ(I) obs: 2.6 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y6N Resolution: 2.81→41.76 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.61
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→41.76 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|