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- PDB-4f1u: Subatomic resolution structure of a high affinity periplasmic pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f1u | |||||||||
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Title | Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with phosphate at pH 4.5 | |||||||||
![]() | Putative alkaline phosphatase | |||||||||
![]() | PHOSPHATE-BINDING PROTEIN / venus flytrap / phosphate binding protein / pstS / DING | |||||||||
Function / homology | ![]() phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liebschner, D. / Elias, M. / Tawfik, D.S. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E. | |||||||||
![]() | ![]() Title: The molecular basis of phosphate discrimination in arsenate-rich environments. Authors: Elias, M. / Wellner, A. / Goldin-Azulay, K. / Chabriere, E. / Vorholt, J.A. / Erb, T.J. / Tawfik, D.S. #1: Journal: J.Am.Chem.Soc. / Year: 2009 Title: Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography. Authors: Liebschner, D. / Elias, M. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 369.4 KB | Display | ![]() |
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PDB format | ![]() | 303.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.1 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f18C ![]() 4f19C ![]() 4f1vC ![]() 3g62 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39119.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PI / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 4% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→36.69 Å / Num. obs: 185558 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3G62 ![]() 3g62 Resolution: 0.98→36.69 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.338 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 8.948 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1.005 Å / Total num. of bins used: 20
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