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- PDB-7qi9: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qi9 | ||||||
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Title | Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.2 in complex with UDP | ||||||
![]() | Glucosyl-3-phosphoglycerate synthase | ||||||
![]() | TRANSFERASE / Glucose / UDP / thermostable / GTA-fold | ||||||
Function / homology | glucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / nucleotide binding / metal ion binding / URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.2 in complex with UDP Authors: Silva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419.8 KB | Display | ![]() |
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PDB format | ![]() | 286.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qpcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35151.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The C-terminal KLAAALEHHHHHH sequence corresponds to a linker followed by an hexahistidine tag used for protein purification Source: (gene. exp.) ![]() Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: ![]() ![]() References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M Potassium Sodium Tartrate pH 7.2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96112 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→50 Å / Num. obs: 171306 / % possible obs: 95.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.79 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.23→1.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13931 / Rpim(I) all: 0.357 / Rrim(I) all: 0.716 / % possible all: 80.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QPC Resolution: 1.23→48.4 Å / SU ML: 0.1073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.9628 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→48.4 Å
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Refine LS restraints |
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LS refinement shell |
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