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- PDB-7pvl: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pvl | ||||||
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Title | Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 - apo form | ||||||
![]() | 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 / 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 8.5 - apo form Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / 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 | ![]() | 301.9 KB | Display | ![]() |
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PDB format | ![]() | 202.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 434.6 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p5lS 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: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 0.2 M MgCl2; 25% 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: 1.43→50 Å / Num. obs: 113499 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.03 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10985 / Rpim(I) all: 0.407 / Rrim(I) all: 0.871 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7P5L Resolution: 1.43→48.15 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7773 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: 20.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→48.15 Å
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Refine LS restraints |
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LS refinement shell |
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