+Open data
-Basic information
Entry | Database: PDB / ID: 1a99 | ||||||
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Title | PUTRESCINE RECEPTOR (POTF) FROM E. COLI | ||||||
Components | PUTRESCINE-BINDING PROTEIN | ||||||
Keywords | BINDING PROTEIN / TRANSPORT / PERIPLASMIC PUTRESCINE BINDING PROTEIN (POTF) | ||||||
Function / homology | Function and homology information putrescine transport / putrescine binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Vassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity. Authors: Vassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Analysis of the Periplasmic Receptor (Potf) of the Putrescine Transport System in Escherichia Coli Authors: Vassylyev, D.G. / Kashiwagi, T. / Tomitori, H. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Characteristics of the Operon for a Putrescine Transport System that Maps at 19 Minutes on the Escherichia Coli Chromosome Authors: Pistocchi, R. / Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Sadakata, Y. / 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 | 1a99.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a99.ent.gz | 233.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a99 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a99 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 38299.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KK313 / Cellular location: PERIPLASM / Gene: PUCPOTF / Plasmid: PMWPOTF / Gene (production host): PUCPOTF / Production host: Escherichia coli (E. coli) / Strain (production host): KK313POTF\:\:KM / References: UniProt: P31133 #2: Chemical | ChemComp-PUT / #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: 3.17 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging dropDetails: Vassylyev, D.G., (1998) Acta Crystallogr.,Sect.D, 54, 132. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 40 Å2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 87495 / % possible obs: 94 % / Num. measured all: 273045 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 2.2→30 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev Biso : 6.5 Å2 / Rms dev position: 1 Å / Weight Biso : 1 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 90790 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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