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Open data
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Basic information
Entry | Database: PDB / ID: 1qhw | |||||||||
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Title | PURPLE ACID PHOSPHATASE FROM RAT BONE | |||||||||
![]() | PROTEIN (PURPLE ACID PHOSPHATASE) | |||||||||
![]() | HYDROLASE / METAL PHOSPHATASE | |||||||||
Function / homology | ![]() Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / response to L-ascorbic acid / acid phosphatase / acid phosphatase activity / cellular response to zinc ion starvation / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production ...Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / response to L-ascorbic acid / acid phosphatase / acid phosphatase activity / cellular response to zinc ion starvation / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / negative regulation of cell adhesion / response to cholesterol / superoxide anion generation / bone morphogenesis / negative regulation of interleukin-1 beta production / response to zinc ion / negative regulation of tumor necrosis factor production / bone resorption / multicellular organismal response to stress / response to mechanical stimulus / nitric oxide biosynthetic process / ossification / ferric iron binding / osteoclast differentiation / response to cytokine / ferrous iron binding / response to insulin / response to organic cyclic compound / negative regulation of inflammatory response / response to ethanol / response to lipopolysaccharide / lysosome / hydrolase activity / defense response to Gram-positive bacterium / positive regulation of cell migration / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lindqvist, Y. / Johansson, E. / Kaija, H. / Vihko, P. / Schneider, G. | |||||||||
![]() | ![]() Title: Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center. Authors: Lindqvist, Y. / Johansson, E. / Kaija, H. / Vihko, P. / Schneider, G. #1: ![]() Title: Tartrate-Resistant Bone Acid Phosphatase: Large-Scale Production and Purification of the Recombinant Enzyme, Characterization, and Crystallization Authors: Kaija, H. / Jia, J. / Lindqvist, Y. / Andersson, G. / Vihko, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.9 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kbpS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 36769.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GLYCOSIDIC LINK BETWEEN ASN 118 AND NAG 344 GLYCOSIDIC LINK BETWEEN NAG 344 AND NAG 345 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 , 4 types, 109 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Kaija, H., (1999) J.Bone Miner.Res., 14, 424. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7816 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 17244 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.2 / % possible all: 84.4 |
Reflection | *PLUS Num. measured all: 63605 |
Reflection shell | *PLUS % possible obs: 84.4 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: BASED ON PDB ENTRY 4KBP Resolution: 2.2→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1502012.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Rfactor Rfree: 0.317 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.264 / Rfactor obs: 0.264 |