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- PDB-4aro: Hafnia Alvei phytase in complex with myo-inositol hexakis sulphate -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aro | |||||||||
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Title | Hafnia Alvei phytase in complex with myo-inositol hexakis sulphate | |||||||||
![]() | HISTIDINE ACID PHOSPHATASE | |||||||||
![]() | HYDROLASE / 6-PHYTASE / MYO-INOSITOL HEXAKIS PHOSPHATE PHOSPHOHYDROLASE / HAPP | |||||||||
Function / homology | ![]() sugar-phosphatase activity / acid phosphatase activity / lysosome organization / dephosphorylation / outer membrane-bounded periplasmic space / lysosome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Moroz, O.V. / Blagova, E.B. / Ariza, A. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. ...Moroz, O.V. / Blagova, E.B. / Ariza, A. / 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 | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 144.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4arsSC ![]() 4aruC ![]() 4arvC S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 45307.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-446 / Mutation: YES 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 | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Sequence details | EUROPEAN NUCLEOTIDE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 40MG/ML PROTEIN IN 50MM SODIUM ACETATE PH 4.5 WITH 5 MM MIHS IN 50 MM SODIUM ACETATE PH 4.5 IN JCSG CONDITION 12 0.04 M KH2PO4 16% PEG 8K 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→41.9 Å / Num. obs: 54630 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.12 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ARS Resolution: 1.59→41.94 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.858 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 |
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Refinement step | Cycle: LAST / Resolution: 1.59→41.94 Å
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Refine LS restraints |
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