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Yorodumi- PDB-6isn: Phosphoglycerate mutase 1 complexed with a small molecule inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6isn | ||||||
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Title | Phosphoglycerate mutase 1 complexed with a small molecule inhibitor | ||||||
Components | Phosphoglycerate mutase 1 | ||||||
Keywords | ISOMERASE / Phosphoglycerate mutase 1 | ||||||
Function / homology | Function and homology information bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å | ||||||
Authors | Jiang, L.L. / Zhou, L. / Huang, K. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Phosphoglycerate mutase 1 complexed with a small molecule inhibitor Authors: Jiang, L.L. / Zhou, L. / Huang, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6isn.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isn.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 6isn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6isn_validation.pdf.gz | 856.9 KB | Display | wwPDB validaton report |
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Full document | 6isn_full_validation.pdf.gz | 859.7 KB | Display | |
Data in XML | 6isn_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6isn_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isn ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26761.350 Da / Num. of mol.: 2 / Fragment: UNP residues 2-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1 / Production host: Escherichia coli (E. coli) References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-MES / | #4: Chemical | ChemComp-AW6 / | #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: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES, pH 6.0, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97851 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97851 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 50593 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.881 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.98→38.89 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→38.89 Å
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Refine LS restraints |
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LS refinement shell |
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