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Yorodumi- PDB-4bqe: Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bqe | ||||||
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Title | Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2) | ||||||
Components | ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / TRANSFERASEE / INHIBITORS / CARBOHYDRATE METABOLISM / ALPHA-1 / SELF-ASSEMBLY ON SURFACES / SURFACE PLASMON RESONANCE / GOLD NANOPARTICLES | ||||||
Function / homology | Function and homology information 1,4-alpha-oligoglucan phosphorylase activity / response to water deprivation / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / chloroplast / pyridoxal phosphate binding / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | O'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A. | ||||||
Citation | Journal: Chem.Sci. / Year: 2014 Title: Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials Authors: O'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bqe.cif.gz | 699.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bqe.ent.gz | 573.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bqe_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 4bqe_full_validation.pdf.gz | 505.5 KB | Display | |
Data in XML | 4bqe_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 4bqe_validation.cif.gz | 117.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqe ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqe | HTTPS FTP |
-Related structure data
Related structure data | 4bqfC 4bqiC 1gpbS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 99064.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET151-PHS2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 PLYSS / References: UniProt: Q9SD76, glycogen phosphorylase |
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-Non-polymers , 5 types, 1853 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLYSequence details | A 33-RESIDUE HEXAHISTIDINE AFFINITY TAG IS APPENDED TO THE N-TERMINUS OF THE WILD-TYPE SEQUENCE AND ...A 33-RESIDUE HEXAHISTID | |
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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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML ...Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML IN 12.5 MM HEPES PH 7.5, 25 MM NACL WAS MIXED WITH 1 MICROLITRE OF THE WELL SOLUTION TO GIVE THE FINAL DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.971 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.971 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.11 Å / Num. obs: 190517 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GPB Resolution: 1.7→90.2 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.442 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→90.2 Å
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Refine LS restraints |
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