+Open data
-Basic information
Entry | Database: PDB / ID: 5lrb | |||||||||
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Title | Plastidial phosphorylase from Barley in complex with acarbose | |||||||||
Components | Alpha-1,4 glucan phosphorylase | |||||||||
Keywords | TRANSFERASE / Starch / phophorylase / plastidial | |||||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / pyridoxal phosphate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Hordeum vulgare var. distichum (barley) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Cuesta-Seijo, J.A. / Ruzanski, C. / Kruzewicz, K. / Palcic, M.M. | |||||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development. Authors: Cuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, K. / Meier, S. / Hagglund, P. / Svensson, B. / Palcic, M.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lrb.cif.gz | 689.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lrb.ent.gz | 569.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lrb ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lrb | HTTPS FTP |
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-Related structure data
Related structure data | 5lr8SC 5lraC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 69 - 968 / Label seq-ID: 27 - 926
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-Components
#1: Protein | Mass: 106013.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare var. distichum (barley) Production host: Escherichia coli (E. coli) / References: UniProt: F2E0G2, glycogen phosphorylase #2: Polysaccharide | #3: Sugar | #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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 30% PEG4000, 0.1M Nacitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 43219 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 0.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LR8 Resolution: 2.9→48.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 45.193 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.706 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→48.92 Å
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Refine LS restraints |
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