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Yorodumi- PDB-5f9c: Crystal structure of the G121R mutant of human phosphoglucomutase 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f9c | ||||||
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Title | Crystal structure of the G121R mutant of human phosphoglucomutase 1 | ||||||
Components | Phosphoglucomutase-1PGM1 | ||||||
Keywords | ISOMERASE / isomerase metabolism | ||||||
Function / homology | Function and homology information Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / Neutrophil degranulation / magnesium ion binding / extracellular exosome / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Beamer, L.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency. Authors: Stiers, K.M. / Kain, B.N. / Graham, A.C. / Beamer, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9c.cif.gz | 426.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9c.ent.gz | 351.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9c ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9c | HTTPS FTP |
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-Related structure data
Related structure data | 5epcSC 5hshC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61619.027 Da / Num. of mol.: 2 / Mutation: G121R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.97 Å3/Da / Density % sol: 58.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.5 M ammonium sulfate with 0.15 lithium sulfate and 0.1 CAPS buffer, pH 10.5 PH range: 10.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→60.943 Å / Num. obs: 71761 / % possible obs: 99.8 % / Redundancy: 14.1 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 12.4 % / Rmerge(I) obs: 3.101 / Mean I/σ(I) obs: 0.8 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Starting model: 5EPC Resolution: 2.5→60.943 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.33 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→60.943 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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