+Open data
-Basic information
Entry | Database: PDB / ID: 3ttk | ||||||
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Title | Crystal structure of apo-SpuD | ||||||
Components | Polyamine transport protein | ||||||
Keywords | TRANSPORT PROTEIN / polyamine receptor / polyamine binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||
Authors | Wu, D.H. / Lim, S.C. / Song, H.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ttk.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ttk.ent.gz | 164.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ttk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/3ttk ftp://data.pdbj.org/pub/pdb/validation_reports/tt/3ttk | HTTPS FTP |
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-Related structure data
Related structure data | 3ttlC 3ttmSC 3ttnC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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.) Pseudomonas aeruginosa (bacteria) / Gene: spuD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6J1 #2: 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: 2.58 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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