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- PDB-6gj2: PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - COMPLEX WITH INOSITOL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gj2 | |||||||||
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Title | PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - COMPLEX WITH INOSITOL HEXASULPHATE | |||||||||
![]() | Purple acid phosphatase | |||||||||
![]() | HYDROLASE / EC 3.1.3.26 / PURPLE ACID PHYTASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Faba-Rodriguez, R. / Brearley, C.A. / Hemmings, A.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants. Authors: Faba-Rodriguez, R. / Gu, Y. / Salmon, M. / Dionisio, G. / Brinch-Pedersen, H. / Brearley, C.A. / Hemmings, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.2 KB | Display | ![]() |
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PDB format | ![]() | 189.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gitSC ![]() 6gizC ![]() 6gjaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57549.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C4PKL0, UniProt: F6MIW5*PLUS, acid phosphatase |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 304 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IHS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IHS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PGE / #7: Chemical | ChemComp-PO4 / | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-IHS / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % / Description: CUBIC |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M SODIUM THIOCYANATE; 20% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2017 | |||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.68→48.51 Å / Num. obs: 71415 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.032 / Rrim(I) all: 0.071 / Net I/σ(I): 12.6 / Num. measured all: 363817 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5.1 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GIT Resolution: 1.68→38.437 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 18.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.25 Å2 / Biso mean: 37.3173 Å2 / Biso min: 18.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→38.437 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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