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Yorodumi- PDB-1fc0: HUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fc0 | ||||||
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Title | HUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE | ||||||
Components | GLYCOGEN PHOSPHORYLASE, LIVER FORM | ||||||
Keywords | TRANSFERASE / phosphorylated protein / allosteric / glucose analog / inhibitor | ||||||
Function / homology | Function and homology information vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / glycogen catabolic process / bile acid binding / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.M. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core. Authors: Rath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.N. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fc0.cif.gz | 333.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fc0.ent.gz | 267.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fc0_validation.pdf.gz | 493.5 KB | Display | wwPDB validaton report |
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Full document | 1fc0_full_validation.pdf.gz | 533.1 KB | Display | |
Data in XML | 1fc0_validation.xml.gz | 59 KB | Display | |
Data in CIF | 1fc0_validation.cif.gz | 80.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fc0 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fc0 | HTTPS FTP |
-Related structure data
Related structure data | 1fa9SC 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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Details | The biological assembly is a dimer related by a two fold NCS axis. Monomer 1 consists of residues A23-A831, monomer 2 consists of residues A1023-A1831. |
-Components
#1: Protein | Mass: 97145.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PBLUEBAC III / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase #2: Sugar | #3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.96 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NaMES, MPD, N-acetyl-beta-D-glycopyranosylamine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 17K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 82210 / Num. obs: 81720 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.3 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.174 / % possible all: 97.8 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FA9 Resolution: 2.4→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 549432.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.63 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.283 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.268 |