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Yorodumi- PDB-4dsy: Crystal structure of red kidney bean purple acid phosphatase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dsy | |||||||||
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Title | Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge fragment CC24201 | |||||||||
Components | Purple acid phosphatase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / phosphatase / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Phaseolus vulgaris (French bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Feder, D. / Hussein, W.M. / Clayton, D.J. / Kan, M. / Schenk, G. / McGeary, R.P. / Guddat, L.W. | |||||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2012 Title: Identification of purple acid phosphatase inhibitors by fragment-based screening: promising new leads for osteoporosis therapeutics. Authors: Feder, D. / Hussein, W.M. / Clayton, D.J. / Kan, M.W. / Schenk, G. / McGeary, R.P. / Guddat, L.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dsy.cif.gz | 391.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dsy.ent.gz | 325.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dsy_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 4dsy_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 4dsy_validation.xml.gz | 78.1 KB | Display | |
Data in CIF | 4dsy_validation.cif.gz | 112.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/4dsy ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4dsy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 / Fragment: unp residues 34-459 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: pap References: UniProt: O24319, UniProt: P80366*PLUS, acid phosphatase |
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-Sugars , 3 types, 16 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 8 types, 1400 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-FE / #6: Chemical | ChemComp-0LO / | #7: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-EDO / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.45 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99.663 Å / Num. obs: 125955 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.864 Å / SU ML: 0.27 / σ(F): 1.05 / Phase error: 18.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.134 Å2 / ksol: 0.356 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.864 Å
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Refine LS restraints |
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LS refinement shell |
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