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- PDB-7o5z: Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o5z | |||||||||
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Title | Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state | |||||||||
![]() | 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 | ![]() | 246.3 KB | Display | ![]() |
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PDB format | ![]() | 162 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.2 KB | Display | ![]() |
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Full document | ![]() | 1012.5 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o0cSC ![]() 7o1bC ![]() 7o4gC ![]() 7o58C 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 , 1 types, 2 molecules AB
#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 Bears mutation T237M Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 258 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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 in 20 mM Hepes pH 7.5 and 0.2 M NaCl. ...Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein 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: 2.07→61.43 Å / Num. obs: 34061 / % possible obs: 98.3 % / Redundancy: 16.5 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.034 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2617 / CC1/2: 0.61 / Rpim(I) all: 0.422 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7O0C Resolution: 2.07→61.43 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5313 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: 39.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→61.43 Å
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Refine LS restraints |
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LS refinement shell |
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