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Yorodumi- PDB-1e4o: Phosphorylase recognition and phosphorolysis of its oligosacchari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e4o | |||||||||
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Title | Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question | |||||||||
Components | MALTODEXTRIN PHOSPHORYLASE | |||||||||
Keywords | HYDROLASE / MALTOPENTAOSE / CARBOHYDRATE RECOGNITION / PHOSPHORYLASE / BINARY AND TERNARY OLIGOSACCHARIDE COMPLEXES | |||||||||
Function / homology | Function and homology information maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Watson, K.A. / McCleverty, C. / Geremia, S. / Cottaz, S. / Driguez, H. / Johnson, L.N. | |||||||||
Citation | Journal: Embo J. / Year: 1999 Title: Phosphorylase Recognition and Phosphorylysis of its Oligosaccharide Substrate: Answers to a Long Outstanding Question Authors: Watson, K.A. / Mccleverty, C. / Geremia, S. / Cottaz, S. / Driguez, H. / Johnson, L.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e4o.cif.gz | 328.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e4o.ent.gz | 271.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e4o_validation.pdf.gz | 522.4 KB | Display | wwPDB validaton report |
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Full document | 1e4o_full_validation.pdf.gz | 618.9 KB | Display | |
Data in XML | 1e4o_validation.xml.gz | 46 KB | Display | |
Data in CIF | 1e4o_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e4o ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e4o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.668458, 0.739024, 0.083707), Vector: |
-Components
#1: Protein | Mass: 90496.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Plasmid: PMAP101 / Strain: DELTA MAL518 / References: UniProt: P00490, glycogen phosphorylase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.34 Å3/Da / Density % sol: 47.34 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: CO-CRYSTALS OBTAINED FROM A SREEN OF: 26-32% 4K PEG, 0.1-0.6 M LICL, 0.1M TRIS/HCL PH8.5 + G5 (FROM 100MM STOCK)ADDED TO THE HANGING DROP (SEE PUBLICATION FOR DETAILS), pH 8.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 38437 / % possible obs: 79.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.18 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 2.2 % / % possible all: 75.1 |
Reflection | *PLUS Num. measured all: 74406 |
Reflection shell | *PLUS % possible obs: 75.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: STRICT NCS APPLIED DISORDERED REGIONS WERE BASED ON THE HIGH RESOLUTION TERNARY COMPLEX AND THE ANALOGOUS BINARY COMPLEX (GSG4-MALP). SEE PUBLICATION FOR DETAILS.
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Displacement parameters | Biso mean: 54.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.1 Å / Total num. of bins used: 10 / % reflection obs: 75.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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