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Yorodumi- PDB-1qm5: Phosphorylase recognition and phosphorylysis of its oligosacchari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qm5 | |||||||||
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Title | Phosphorylase recognition and phosphorylysis of its oligosaccharide substrate: answers to a long outstanding question | |||||||||
Components | MALTODEXTRIN PHOSPHORYLASE | |||||||||
Keywords | PHOSPHORYLASE / THIO-OLIGOSACCHARIDE / PHOSPHOROLYSIS / MALP / GLYCOSYLTRANSFERASE | |||||||||
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 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 Phosphorolysis 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 | 1qm5.cif.gz | 337.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qm5.ent.gz | 274 KB | Display | PDB format |
PDBx/mmJSON format | 1qm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qm5_validation.pdf.gz | 570 KB | Display | wwPDB validaton report |
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Full document | 1qm5_full_validation.pdf.gz | 622.3 KB | Display | |
Data in XML | 1qm5_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 1qm5_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qm5 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qm5 | 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: (-0.999928, -0.011762, 0.002474), Vector: Details | THE ASYMMETRIC UNIT CONTAINS THE DIMERIC COMPLEX | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 90496.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CO-FACTOR PLP (RESID 999) LINKED TO LYS645 (K680 RABBIT MUSCLE NUMBERING) Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cell line: DELTA MALA518 / Cellular location: CYTOPLASM / Plasmid: PMAP101 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DELTA MALA518 / References: UniProt: P00490, glycogen phosphorylase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 758 molecules
#3: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | COVALENT ATTACHMENT OF PYRIDOXAL PHOSPHATE TO LYS 645. THE PDB FILE HAS BEEN LABELED ACCORDING TO ...COVALENT ATTACHMENT |
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Sequence details | THE SWISSPROT SEQUENCE P00490 (PHSM_ECOLI) IS FROM REFERENCE D.PALM D,R.GOERL,G.WEIDINGER,R.ZEIER,B. ...THE SWISSPROT SEQUENCE P00490 (PHSM_ECOLI) IS FROM REFERENCE D.PALM D,R.GOERL,G.WEIDINGER,R.ZEIER,B.FISCHER,R.SCHINZEL R. E. COLI MALTODEXTR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: (26-32)% PEG 4000, (0.1-0.6)M LICL, 0.1M TRIS/HCL PH8.5, 18 DEG C, HANGING DROP, 10MG/ML PROTEIN, 20MM GSG4, 50MM PHOSPHATE, 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: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS/WIGGLER |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 72681 / % possible obs: 80 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.1 % / % possible all: 64.5 |
Reflection | *PLUS Num. measured all: 152192 |
Reflection shell | *PLUS % possible obs: 64.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: STRICT NCS APPLIED
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Displacement parameters | Biso mean: 34.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Total num. of bins used: 10 / % reflection obs: 64.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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