[English] 日本語
Yorodumi- PDB-1l5w: Crystal Structure of the Maltodextrin Phosphorylase Complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l5w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Maltodextrin Phosphorylase Complexed with the Products of the Enzymatic Reaction between Glucose-1-phosphate and Maltotetraose | |||||||||
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: 1.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1l5w.cif.gz | 348.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1l5w.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l5w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1l5w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1l5w_validation.xml.gz | 66.7 KB | Display | |
Data in CIF | 1l5w_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5w ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5w | HTTPS FTP |
-Related structure data
Related structure data | 1l5vSC 1l6iC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, TRIS, Lithium Chloride, Glucose-1-phosphate., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 24, 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: 1.8→17 Å / Num. all: 134845 / Num. obs: 134845 / % possible obs: 85 % / Redundancy: 7.8 % / Biso Wilson estimate: 21.633 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / Num. unique all: 16882 / % possible all: 73.6 |
Reflection | *PLUS Lowest resolution: 17 Å / Num. measured all: 1056617 |
Reflection shell | *PLUS % possible obs: 73.6 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1L5V Resolution: 1.8→20 Å / SU B: 5.6336 / SU ML: 0.16158 / Cross valid method: THROUGHOUT / ESU R: 0.15815 / ESU R Free: 0.13805 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.262 Å2
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.187 / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 1.7 |