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Yorodumi- PDB-5tpq: E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tpq | ||||||
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Title | E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant | ||||||
Components | Alkaline phosphatase | ||||||
Keywords | HYDROLASE / Alkaline Phosphatase / generalist enzyme / bimetallo motif / catalytic promiscuity / evolution / D101A/D153A/R166S/E322A/K328A | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Sunden, F. / AlSadhan, I. / Lyubimov, A.Y. / Doukov, T. / Swan, J. / 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 | 5tpq.cif.gz | 348.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tpq.ent.gz | 284.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tpq_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 5tpq_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 5tpq_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 5tpq_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpq ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpq | HTTPS FTP |
-Related structure data
Related structure data | 5tooC 3tg0S 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: 46560.742 Da / Num. of mol.: 2 / Fragment: UNP residues 30-471 / Mutation: D101A, D153A, R166S, E322A, K328A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: phoA, b0383, JW0374 / Production host: Escherichia coli (E. coli) / Strain (production host): SM547lambdaDE3 / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: Small cube |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 5 mg/mL protein in 10 mM MOPS pH 7.0, 50 mM NaCl, 100 mM ZnCl2. Protein solution mixed with equal volume of precipitant solution: 23% PEG 3350, 0.2 M NH3F, 0.2 M HEPES pH=8.0 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cryo |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→38.6 Å / Num. obs: 39204 / % possible obs: 99.5 % / Redundancy: 35.5 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.594 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 30.4 % / Rmerge(I) obs: 5.6 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.318 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TG0 Resolution: 2.45→38.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0.03 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.375 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.227
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Displacement parameters | Biso mean: 55.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→38.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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