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Yorodumi- PDB-5lra: Plastidial phosphorylase PhoI from barley in complex with maltote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lra | |||||||||
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Title | Plastidial phosphorylase PhoI from barley in complex with maltotetraose | |||||||||
Components | Alpha-1,4 glucan phosphorylase | |||||||||
Keywords | TRANSFERASE / Starch / phosphorylase / plastidial | |||||||||
Function / homology | Function and homology information response to water deprivation / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / response to temperature stimulus / pyridoxal phosphate binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Hordeum vulgare var. distichum (barley) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Cuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, 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 | 5lra.cif.gz | 697.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lra.ent.gz | 576.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lra_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5lra_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5lra_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 5lra_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lra ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lra | HTTPS FTP |
-Related structure data
Related structure data | 5lr8C 5lrbSC 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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-Components
#1: Protein | Mass: 106013.734 Da / Num. of mol.: 2 / Fragment: UNP residues 44-968 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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #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: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG4000, 0.1M Na Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 38803 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.13 / Num. unique all: 6756 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LRB Resolution: 3→49.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 47.956 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / 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: 90.192 Å2
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Refinement step | Cycle: 1 / Resolution: 3→49.39 Å
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Refine LS restraints |
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