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Yorodumi- PDB-1l6i: Crystal Structure of the Maltodextrin Phosphorylase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l6i | |||||||||
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Title | Crystal Structure of the Maltodextrin Phosphorylase complexed with the products of the enzymatic reaction between glucose-1-phosphate and maltopentaose | |||||||||
Components | MALTODEXTRIN PHOSPHORYLASE | |||||||||
Keywords | TRANSFERASE / phosphorylase / enzymatic catalysis / substrate complex | |||||||||
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 / FOURIER SYNTHESIS / Resolution: 2.2 Å | |||||||||
Authors | Geremia, S. / Campagnolo, M. / Schinzel, R. / Johnson, L.N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase Authors: Geremia, S. / Campagnolo, M. / Schinzel, R. / 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 | 1l6i.cif.gz | 353.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6i.ent.gz | 284.8 KB | Display | PDB format |
PDBx/mmJSON format | 1l6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l6i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1l6i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1l6i_validation.xml.gz | 74 KB | Display | |
Data in CIF | 1l6i_validation.cif.gz | 107 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6i ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6i | HTTPS FTP |
-Related structure data
Related structure data | 1l5vSC 1l5wC 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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-Components
#1: Protein | Mass: 90547.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMAP101 / Production host: Escherichia coli (E. coli) / Strain (production host): DELTA MALA518 References: GenBank: 606352, UniProt: P00490*PLUS, 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: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: peg 4000, t / pH: 8.5 Details: PEG 4000, TRIS, Lithium Chloride, Glucose-1-phosphate, pH 8.5, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
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: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19 Å / Num. all: 81626 / Num. obs: 81626 / % possible obs: 91.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.034 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11231 / % possible all: 87.4 |
Reflection | *PLUS Lowest resolution: 19 Å / Num. measured all: 413101 |
Reflection shell | *PLUS % possible obs: 87.4 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1L5V Resolution: 2.2→20 Å / SU B: 7.6643 / SU ML: 0.19493 / Cross valid method: THROUGHOUT / ESU R: 0.36121 / ESU R Free: 0.23644 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.156 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 78791 / Rfactor obs: 0.2 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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