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Yorodumi- PDB-1poy: SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1poy | ||||||
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Title | SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM) | ||||||
Components | SPERMIDINE/PUTRESCINE-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / BINDING PROTEIN | ||||||
Function / homology | Function and homology information spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine transport / putrescine binding / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Sugiyama, S. / Vassylyev, D.G. / Matsushima, M. / Morikawa, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli. Authors: Sugiyama, S. / Vassylyev, D.G. / Matsushima, M. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #1: Journal: To be Published Title: Crystallization and Preliminary X-Ray Analysis of the Primary Receptor (Potd) of the Polyamine Transport System in Escherichia Coli Authors: Sugiyama, S. / Matsushima, M. / Saisho, T. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Functions of Pota and Potd Proteins in Spermidine-Preferential Uptake System in Escherichia Coli Authors: Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Kobayashi, H. / Igarashi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1poy.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1poy.ent.gz | 209.5 KB | Display | PDB format |
PDBx/mmJSON format | 1poy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1poy ftp://data.pdbj.org/pub/pdb/validation_reports/po/1poy | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36297.879 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: THE POLYAMINE TRANSPORT GENES IN ESCHERICHIA COLI HAD BEEN CLONED AND WAS PREVIOUSLY DESCRIBED (KASHIWAGI ET AL., (1990) J.BIOL.CHEM. 265\:20893-20897, KASHIWAGI ET AL., (1991) J.BIOL.CHEM. 266\:20922-20927) Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23861, UniProt: P0AFK9*PLUS #2: Chemical | ChemComp-SPD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 45 % |
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Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→300 Å / Num. obs: 38903 / % possible obs: 81.6 % / Observed criterion σ(I): 1 |
Reflection | *PLUS Rmerge(I) obs: 0.0679 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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