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Open data
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Basic information
Entry | Database: PDB / ID: 4ars | ||||||
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Title | Hafnia Alvei phytase apo form | ||||||
![]() | HISTIDINE ACID PHOSPHATASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() sugar-phosphatase activity / acid phosphatase activity / lysosome organization / outer membrane-bounded periplasmic space / lysosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ariza, A. / Moroz, O.V. / Blagova, E.B. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. ...Ariza, A. / Moroz, O.V. / Blagova, E.B. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. / Glitsoe, V. / Skov, L.K. / Wilson, K.S. | ||||||
![]() | ![]() Title: Degradation of Phytate by the 6-Phytase from Hafnia Alvei: A Combined Structural and Solution Study. Authors: Ariza, A. / Moroz, O.V. / Blagova, E.V. / Turkenburg, J.P. / Waterman, J. / Roberts, S.M. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. / Glitsoe, V. / Skov, L.K. / Wilson, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.5 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4aroC ![]() 4aruC ![]() 4arvC ![]() 1dklS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45395.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G9Y2J2, UniProt: H9TUK5*PLUS, 4-phytase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE ALSO CORRESPONDS TO THE EUROPEAN NUCLEOTIDE ARCHIVE ENTRY JQ394762. NATURAL ...THE SEQUENCE ALSO CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 48.32 % / Description: NONE |
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Crystal grow | Details: 8MG/ML PROTEIN; 0.1 M HEPES PH 7.5, 10% ISOPROPANOL, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.7 Å / Num. obs: 34671 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DKL Resolution: 1.9→32.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.773 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.55 Å
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Refine LS restraints |
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