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- PDB-7o58: Human phosphomannomutase 2 (PMM2) with mutation T237M in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o58 | |||||||||
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Title | Human phosphomannomutase 2 (PMM2) with mutation T237M in complex with the activator glucose 1,6-bisphosphate | |||||||||
![]() | Phosphomannomutase 2 | |||||||||
![]() | ISOMERASE / glycobiology / congenital disorders of glycosylation / phosphotransferase / phosphomutase | |||||||||
Function / homology | ![]() Defective PMM2 causes PMM2-CDG / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / neuronal cell body / nucleoplasm ...Defective PMM2 causes PMM2-CDG / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / neuronal cell body / nucleoplasm / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramon-Maiques, S. / Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Perez, B. / Rubio, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures. Authors: Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Velazquez-Campoy, A. / Rubio, V. / Perez, B. / Ramon-Maiques, 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 | ![]() | 253.2 KB | Display | ![]() |
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PDB format | ![]() | 166.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o0cSC ![]() 7o1bC ![]() 7o4gC ![]() 7o5zC 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/G16.gif)
![](data/chem/img/G16.gif)
#1: Protein | Mass: 28304.428 Da / Num. of mol.: 2 / Mutation: T237M Source method: isolated from a genetically manipulated source Details: Residues GPMAAP at the N-terminus are not seen in the electron density map. The most N-terminal GP sequence is part of the fusion tag after cleavage Protein has mutation T237M Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-G16 / | |
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-Non-polymers , 5 types, 314 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein and 3 mM glucose 1,6-bisphophate in 20 ...Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein and 3 mM glucose 1,6-bisphophate in 20 mM Hepes pH 7.5 and 0.2 M NaCl. Crystallization solution contained 0.3-0.4 M MgCl2, 24% PEG3350 and 0.1 M HEPES pH 7.5 |
-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: Jul 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.965→59.95 Å / Num. obs: 37985 / % possible obs: 96.4 % / Redundancy: 18.3 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.042 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.965→2.01 Å / Redundancy: 19.2 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2683 / CC1/2: 0.751 / Rpim(I) all: 0.524 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7O0C Resolution: 1.97→59.95 Å / SU ML: 0.1822 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6521 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: 43.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→59.95 Å
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Refine LS restraints |
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LS refinement shell |
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