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Yorodumi- PDB-7o1b: Human phosphomannomutase 2 (PMM2) wild-type co-crystallized with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o1b | |||||||||
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Title | Human phosphomannomutase 2 (PMM2) wild-type co-crystallized with the activator glucose 1,6-bisphosphate | |||||||||
Components | Phosphomannomutase 2 | |||||||||
Keywords | ISOMERASE / glycobiology / congenital disorders of glycosylation / phosphotransferase / phosphomutase | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | |||||||||
Authors | Ramon-Maiques, S. / Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Perez, B. / Rubio, V. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: J Inherit Metab Dis / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o1b.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o1b.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 7o1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/7o1b ftp://data.pdbj.org/pub/pdb/validation_reports/o1/7o1b | HTTPS FTP |
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-Related structure data
Related structure data | 7o0cSC 7o4gC 7o58C 7o5zC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28274.336 Da / Num. of mol.: 2 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 Source: (gene. exp.) Homo sapiens (human) / Gene: PMM2 / Plasmid: pOPIN-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15305, phosphomannomutase #2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-G16 / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % Description: Crystals of hexagonal morphology and 0.025 mm in the largest dimension |
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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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→61.45 Å / Num. obs: 10988 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.081 / Rrim(I) all: 0.35 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3.08→3.129 Å / Redundancy: 18.6 % / Rmerge(I) obs: 1.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 514 / CC1/2: 0.784 / Rpim(I) all: 0.364 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7O0C Resolution: 3.08→61.45 Å / SU ML: 0.3675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2433 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: 43.24 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→61.45 Å
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Refine LS restraints |
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LS refinement shell |
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