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- PDB-13pk: TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI -
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Open data
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Basic information
Entry | Database: PDB / ID: 13pk | ||||||
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Title | TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI | ||||||
![]() | 3-PHOSPHOGLYCERATE KINASE | ||||||
![]() | KINASE / PHOSPHOGLYCERATE / TERNARY COMPLEX / GLYCOLYSIS / TRANSFERASE | ||||||
Function / homology | ![]() phosphoglycerate kinase / phosphoglycerate kinase activity / glycosome / gluconeogenesis / glycolytic process / ADP binding / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bernstein, B.E. / Michels, P.A.M. / Hol, W.G.J. | ||||||
![]() | ![]() Title: Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Authors: Bernstein, B.E. / Michels, P.A. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.8 KB | Display | ![]() |
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PDB format | ![]() | 270.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 645.4 KB | Display | ![]() |
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Full document | ![]() | 702.6 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 64 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1phpS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44699.984 Da / Num. of mol.: 4 Mutation: TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 615 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-ADP / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 60.87 % / Description: MR SOLUTION USED INDIVIDUAL DOMAINS SEPARATELY | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8 Details: VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion PH range: 7.5-8.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusionDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 73223 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Rsym value: 0.061 |
Reflection shell | Resolution: 2.5→2.53 Å / Rsym value: 0.328 |
Reflection | *PLUS Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Rmerge(I) obs: 0.328 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PHP Resolution: 2.5→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.5→2.53 Å / Total num. of bins used: 25 /
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.338 |