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- PDB-7n3r: The ternary complex of human Bisphosphoglycerate mutase with 3-ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n3r | ||||||
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Title | The ternary complex of human Bisphosphoglycerate mutase with 3-phosphoglycerate and 2-phosphoglycolate | ||||||
![]() | Bisphosphoglycerate mutase | ||||||
![]() | ISOMERASE / BPGM / Bisphosphoglycerate mutase / 2 / 3-bisphosphoglycerate phosphatase / 3-phosphoglycerate / 2-phosphoglycolate / erythrocyte | ||||||
Function / homology | ![]() carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan / oxygen transport / erythrocyte development / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aljahdali, A.S. / Musayev, F.N. / Safo, M.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase. Authors: Aljahdali, A.S. / Musayev, F.N. / Burgner 2nd, J.W. / Ghatge, M.S. / Shekar, V. / Zhang, Y. / Omar, A.M. / Safo, M.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.5 KB | Display | ![]() |
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PDB format | ![]() | 90.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n3sC ![]() 2h4zS S: Starting model for refinement C: citing same article ( |
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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: 31118.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P07738, bisphosphoglycerate mutase, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) #2: Chemical | ChemComp-3PG / | #3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M BIS TRIS propane, 18% polyethylene glycol 8000, 10% v/v polyethylene glycol 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→27.65 Å / Num. obs: 29181 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Rrim(I) all: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2677 / CC1/2: 0.916 / Rpim(I) all: 0.181 / Rrim(I) all: 0.524 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H4Z Resolution: 2.25→27.648 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.24 / Stereochemistry target values: ML
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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 max: 101.32 Å2 / Biso mean: 41.7833 Å2 / Biso min: 13.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→27.648 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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