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Open data
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Basic information
Entry | Database: PDB / ID: 3ttk | ||||||
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Title | Crystal structure of apo-SpuD | ||||||
![]() | Polyamine transport protein | ||||||
![]() | TRANSPORT PROTEIN / polyamine receptor / polyamine binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, D.H. / Lim, S.C. / Song, H.W. | ||||||
![]() | ![]() Title: Structural Basis of Substrate Binding Specificity Revealed by the Crystal Structures of Polyamine Receptors SpuD and SpuE from Pseudomonas aeruginosa Authors: Wu, D.H. / Lim, S.C. / Dong, Y.H. / Wu, J.E. / Tao, F. / Zhou, L. / Zhang, L.H. / Song, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.6 KB | Display | ![]() |
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PDB format | ![]() | 164.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 497.4 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ttlC ![]() 3ttmSC ![]() 3ttnC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38380.617 Da / Num. of mol.: 3 / Fragment: UNP residues 26-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 15, 2009 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 23272 / Num. obs: 23272 / % possible obs: 84.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.9→3.06 Å / % possible all: 80.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TTM Resolution: 2.97→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.853 / SU B: 20.282 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.577 / 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: 39.859 Å2
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Refinement step | Cycle: LAST / Resolution: 2.97→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.97→3.045 Å / Total num. of bins used: 20
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