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- PDB-7p8g: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p8g | ||||||
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Title | Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 - apo form | ||||||
![]() | Glucosyl-3-phosphoglycerate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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 5.5 - 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 | ![]() | 89.8 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 35151.129 Da / Num. of mol.: 1 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, ![]() | ||||||||
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#2: Chemical | ChemComp-CL / ![]() #3: Sugar | ChemComp-BGC / | ![]() #4: Chemical | ChemComp-MLI / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.58 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, 3M NaCl |
-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![]() |
Reflection | Resolution: 2.13→46.6 Å / Num. obs: 34136 / % possible obs: 98.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 46.03 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.056 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.13→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 581 / Rpim(I) all: 0.276 / Rrim(I) all: 0.635 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7P5L Resolution: 2.13→46.6 Å / SU ML: 0.3063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5604 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: 58.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→46.6 Å
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Refine LS restraints |
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LS refinement shell |
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