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- PDB-4f18: 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: 4f18 | ||||||
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Title | Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with arsenate at pH 8.5 | ||||||
![]() | Putative alkaline phosphatase | ||||||
![]() | phosphate-binding protein / pstS / periplasmic binding protein / DING protein | ||||||
Function / homology | ![]() phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elias, M. / Wellner, A. / Goldin, K. / Chabriere, E. / Tawfik, D.S. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 334.7 KB | Display | ![]() |
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PDB format | ![]() | 272.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
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Full document | ![]() | 448.2 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 47 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f19C ![]() 4f1uC ![]() 4f1vC ![]() 3g63 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-8AR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-26% PEG 8000, 200mM Li2SO4, 1mM CaCl2, 100mM arsenate pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→33.02 Å / Num. all: 188778 / Num. obs: 183115 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.29 % / Rsym value: 0.033 / Net I/σ(I): 18.89 |
Reflection shell | Resolution: 0.96→1.05 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 4.06 / Rsym value: 0.255 / % possible all: 87.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3G63 ![]() 3g63 Resolution: 0.96→33.02 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / 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: 9.834 Å2
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Refinement step | Cycle: LAST / Resolution: 0.96→33.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.96→0.985 Å / Total num. of bins used: 20
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