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Yorodumi- PDB-2iuc: Structure of alkaline phosphatase from the Antarctic bacterium TAB5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iuc | ||||||
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Title | Structure of alkaline phosphatase from the Antarctic bacterium TAB5 | ||||||
Components | (ALKALINE PHOSPHATASE) x 2 | ||||||
Keywords | HYDROLASE / ALKALINE PHOSPHATASE / COLD ADAPTATION / PSYCROPHILES | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ANTARCTIC BACTERIUM TAB5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wang, E. / Koutsioulis, D. / Leiros, H.K.S. / Andersen, O.A. / Bouriotis, V. / Hough, E. / Heikinheimo, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of Alkaline Phosphatase from the Antarctic Bacterium Tab5. Authors: Wang, E. / Koutsioulis, D. / Leiros, H.K.S. / Andersen, O.A. / Bouriotis, V. / Hough, E. / Heikinheimo, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iuc.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iuc.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iuc ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iuc | HTTPS FTP |
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-Related structure data
Related structure data | 1ed9S S: Starting model for refinement |
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Similar structure data |
-Links
-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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 40301.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN P ATOM AND S84 IN THE ACTIVE SITE Source: (gene. exp.) ANTARCTIC BACTERIUM TAB5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9KWY4, alkaline phosphatase |
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#2: Protein | Mass: 40161.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN P ATOM AND S84 IN THE ACTIVE SITE Source: (gene. exp.) ANTARCTIC BACTERIUM TAB5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9KWY4, alkaline phosphatase |
-Non-polymers , 5 types, 451 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-CAC / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING-DROP, 4 DEGREE C, 17 MG/ML PROTEIN, 23% PEG3350, 0.2M NAAC, 10MM 4-NITROPHENYL PHOSPHATE, 0.1M CACODYLATE, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 48685 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.3 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ED9 Resolution: 1.95→8.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.481 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5-6 SOME RESIDUES IN CROWN DOMAIN AND 8-10 AT N-TERMINUS HAS NOT BEEN MODELLED DUE TO MISSING ELECTRON DENSITY IN THIS REGIONS.
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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: 19.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→8.74 Å
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Refine LS restraints |
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