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Yorodumi- PDB-4yr1: Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yr1 | ||||||
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Title | Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in complex with inorganic phosphate | ||||||
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 / 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: 2.24 Å | ||||||
Authors | Peck, A. / Herschlag, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2015 Title: Extensive site-directed mutagenesis reveals interconnected functional units in the Alkaline Phosphatase active site. Authors: Sunden, F. / Peck, A. / Salzman, J. / Ressl, 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 | 4yr1.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yr1.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yr1_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 4yr1_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 4yr1_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 4yr1_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/4yr1 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/4yr1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 46267.492 Da / Num. of mol.: 2 / Mutation: D101A D153A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: phoA, b0383, JW0374 / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): SM547(DE3) / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.85 Å3/Da / Density % sol: 56.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 3350, Bis-Tris, ammonium sulfate, glycerol (cryo-protectant) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.24→52.89 Å / Num. obs: 51846 / % possible obs: 100 % / Redundancy: 21.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.438 / Rpim(I) all: 0.096 / Net I/σ(I): 7.8 / Num. measured all: 1117848 / Scaling rejects: 252 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→52.89 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / Matrix type: sparse / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.169 / SU B: 11.297 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 81.86 Å2 / Biso mean: 37.56 Å2 / Biso min: 19.08 Å2
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Refinement step | Cycle: final / Resolution: 2.24→52.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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