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Yorodumi- PDB-3ttn: Crystal structures of polyamine receptors SpuD and SpuE from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ttn | ||||||
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Title | Crystal structures of polyamine receptors SpuD and SpuE from Pseudomonas aeruginosa | ||||||
Components | Polyamine transport protein | ||||||
Keywords | TRANSPORT PROTEIN / polyamine binding protein / spermidine | ||||||
Function / homology | Function and homology information polyamine transport / spermidine binding / periplasmic space / extracellular space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Lim, S.C. / Wu, D.H. / 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 | 3ttn.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ttn.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ttn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ttn_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 3ttn_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 3ttn_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 3ttn_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/3ttn ftp://data.pdbj.org/pub/pdb/validation_reports/tt/3ttn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 37737.875 Da / Num. of mol.: 2 / Fragment: UNP residues 28-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: spuE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6J0 #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 2.6 Details: 0.1M citric acid, 28% PEG 6000, 4% Jeffamine M-600, pH 2.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97988 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97988 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.07 Å / Num. all: 40146 / Num. obs: 40146 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.11 Å / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→23.07 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.527 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.187 / 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: 16.838 Å2
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Refinement step | Cycle: LAST / Resolution: 2→23.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 1 / Number: 2465 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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