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- PDB-6vj7: Crystal structure of red kidney bean purple acid phosphatase in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vj7 | ||||||||||||
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Title | Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine 5'-(beta,gamma imido)triphosphate | ||||||||||||
![]() | Fe(3+)-Zn(2+) purple acid phosphatase | ||||||||||||
![]() | METAL BINDING PROTEIN / Hydrolase / Purple acid phosphatase / metallohydrolases / catalysis / phytase / ATPase / agricultural biotechnology | ||||||||||||
Function / homology | ![]() acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Feder, D. / Schenk, G. / Guddat, L.W. / McGeary, R.P. / Mitic, N. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops. Authors: Feder, D. / McGeary, R.P. / Mitic, N. / Lonhienne, T. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S. / Guddat, L.W. / Schenk, G. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 398.3 KB | Display | ![]() |
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PDB format | ![]() | 322.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 949.3 KB | Display | ![]() |
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Full document | ![]() | 964.7 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6py9C ![]() 4dhlS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49555.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 6 types, 15 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-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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#3: Polysaccharide | #4: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | #6: Polysaccharide | #13: Sugar | ChemComp-NAG / |
-Non-polymers , 11 types, 859 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-ZN / #8: Chemical | ChemComp-FE / #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-EDO / #12: Chemical | ChemComp-PGE / #14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-IPA / | #18: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.19 % / Description: Hexagonal |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.76 Å / Num. obs: 63465 / % possible obs: 74.9 % / Redundancy: 1.62 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1835 / Χ2: 1.11 / % possible all: 50.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DHL Resolution: 2.6→40.76 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.327 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.76 Å
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Refine LS restraints |
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LS refinement shell |
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