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Yorodumi- PDB-5too: Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5too | ||||||
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Title | Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A, R164A mutant | ||||||
Components | Alkaline phosphatase PafA | ||||||
Keywords | HYDROLASE / Alkaline Phosphatase / Phosphomonoesterase / PafA / Weak phosphate binder / Zinc bimetallo core | ||||||
Function / homology | Function and homology information glucose-6-phosphatase activity / glucose-1-phosphatase activity / carbohydrate phosphatase activity / sugar-phosphatase activity / alkaline phosphatase / alkaline phosphatase activity / dephosphorylation / periplasmic space / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.031 Å | ||||||
Authors | Lyubimov, A.Y. / Sunden, F. / AlSadhan, I. / Herschlag, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution. Authors: Sunden, F. / AlSadhan, I. / Lyubimov, A. / Doukov, T. / Swan, J. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5too.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5too.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 5too.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5too_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 5too_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 5too_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5too_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/5too ftp://data.pdbj.org/pub/pdb/validation_reports/to/5too | HTTPS FTP |
-Related structure data
Related structure data | 5tpqC 5tj3S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 61120.406 Da / Num. of mol.: 1 / Fragment: UNP residues 21-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Gene: pafA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJX5, alkaline phosphatase | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 32.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 22% PEG3350, 0.1 M sodium acetate, pH 4.4, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016 |
Radiation | Monochromator: Si(111) Side scattering bent cube-root I-beam single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→41.01 Å / Num. obs: 28568 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.518 / CC1/2: 0.66 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TJ3 Resolution: 2.031→41.009 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.1 Å2 / Biso mean: 40.6973 Å2 / Biso min: 16.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.031→41.009 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %
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