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- PDB-5o7d: The X-ray structure of human R38M phosphoglycerate kinase 1 mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o7d | ||||||
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Title | The X-ray structure of human R38M phosphoglycerate kinase 1 mutant | ||||||
![]() | Phosphoglycerate kinase 1 | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / phosphorylation / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ilari, A. / Fiorillo, A. / Cipollone, A. / Petrosino, M. | ||||||
![]() | ![]() Title: The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme. Authors: Fiorillo, A. / Petrosino, M. / Ilari, A. / Pasquo, A. / Cipollone, A. / Maggi, M. / Chiaraluce, R. / Consalvi, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.3 KB | Display | ![]() |
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PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 749.8 KB | Display | ![]() |
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Full document | ![]() | 749.8 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m1rC ![]() 5m3uC ![]() 5m6zC ![]() 5mxmC ![]() 2x13S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 44646.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG2K-MME 28-34%, bis-tris 0.1M pH 7 / PH range: 6.5-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 31685 / % possible obs: 96.1 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.097 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.84→1.871 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.8 / Num. unique obs: 1650 / CC1/2: 0.367 / Rpim(I) all: 0.501 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2x13 Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.038 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.544 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→50 Å
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Refine LS restraints |
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