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Yorodumi- PDB-2ecp: THE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ecp | |||||||||
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Title | THE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE COMPLEX | |||||||||
Components | MALTODEXTRIN PHOSPHORYLASE | |||||||||
Keywords | ACARBOSE / DIABETES / PHOSPHORYLASE / 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: 2.95 Å | |||||||||
Authors | O'Reilly, M. / Watson, K.A. / Johnson, L.N. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex. Authors: O'Reilly, M. / Watson, K.A. / 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 | 2ecp.cif.gz | 328.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ecp.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ecp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ecp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2ecp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ecp_validation.xml.gz | 66.8 KB | Display | |
Data in CIF | 2ecp_validation.cif.gz | 89 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2ecp ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2ecp | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.666, 0.745, 0.038), Vector: |
-Components
#1: Protein | Mass: 90276.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Tissue: MUSCLE / Cell line: DELTA MALA518 / Cellular location: CYTOPLASM / Plasmid: PMAP101 / Cell line (production host): DELTA MALA518 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00490, glycogen phosphorylase #2: Polysaccharide | #3: Chemical | #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: 2.4 Å3/Da / Density % sol: 55 % Description: MALP NATIVE STRUCTURE USED AS STARTING MODEL FOR MOLECULAR REPLACEMENT. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / 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: ELETTRA / Beamline: 5.2R / Wavelength: 0.9 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: DIAMOND C(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→33.6 Å / Num. obs: 33657 / % possible obs: 88.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.3 / % possible all: 78.2 |
Reflection shell | *PLUS % possible obs: 78.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.57 / Details: TIGHT NCS RESTRAINTS APPLIED
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Displacement parameters | Biso mean: 53.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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