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- PDB-7ov8: Crystal structure of pig purple acid phosphatase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ov8 | |||||||||
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Title | Crystal structure of pig purple acid phosphatase in complex with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and glycerol | |||||||||
![]() | Tartrate-resistant acid phosphatase type 5 | |||||||||
![]() | HYDROLASE / Purple acid phosphatase / metallohydrolases / osteoporosis / fragment-based drug design / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() Vitamin B2 (riboflavin) metabolism / acid phosphatase / acid phosphatase activity / bone resorption / ferric iron binding / ferrous iron binding / iron ion transport / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Feder, D. / McGeary, R.P. / Guddat, L.W. / Schenk, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. Authors: Feder, D. / Mohd-Pahmi, S.H. / Hussein, W.M. / Guddat, L.W. / McGeary, R.P. / 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 | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 75.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.8 MB | Display | ![]() |
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Full document | ![]() | 5.8 MB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ov2C ![]() 7ov3C ![]() 1uteS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 36932.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#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 |
-Non-polymers , 8 types, 450 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EPE / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PGE / | #9: Chemical | #10: 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: 2.22 Å3/Da / Density % sol: 44.61 % / Description: Rod-shaped purple crystals |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25% (W/V) PEG3350, 0.1 M LICL, 5% (V/V)ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.0, PROTEIN CONCENTRATION 38 MG/ML |
-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: Nov 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48 Å / Num. obs: 15124 / % possible obs: 99.3 % / Redundancy: 3.64 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.163 / Χ2: 0.95 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.3→2.48 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique obs: 2896 / Χ2: 1.03 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UTE Resolution: 2.3→39.57 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 27.1728 / Stereochemistry target values: 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: 33.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.57 Å
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Refine LS restraints |
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LS refinement shell |
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