+Open data
-Basic information
Entry | Database: PDB / ID: 5c66 | ||||||
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Title | E. Coli Alkaline Phosphatase in complex with tungstate | ||||||
Components | Alkaline phosphatase | ||||||
Keywords | HYDROLASE | ||||||
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 / dephosphorylation / 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: 2.03 Å | ||||||
Authors | Peck, A. / Herschlag, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase. Authors: Peck, A. / Sunden, F. / Andrews, L.D. / Pande, V.S. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c66.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c66.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 5c66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/5c66 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c66 | HTTPS FTP |
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-Related structure data
Related structure data | 3tg0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 10 - 447 / Label seq-ID: 10 - 447
NCS oper:
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-Components
#1: Protein | Mass: 48294.699 Da / Num. of mol.: 2 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): BL21(DE3) / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium MOPS, sodium chloride, zinc chloride, magnesium chloride, PEG3350, ammonium fluoride, sodium tungstate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→52.74 Å / Num. all: 64098 / Num. obs: 64098 / % possible obs: 93.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.9 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TG0 Resolution: 2.03→52.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.712 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 | Biso mean: 40.057 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→52.74 Å
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Refine LS restraints |
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