+Open data
-Basic information
Entry | Database: PDB / ID: 1a0t | |||||||||
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Title | SUCROSE-SPECIFIC PORIN, WITH BOUND SUCROSE MOLECULES | |||||||||
Components | SUCROSE-SPECIFIC PORIN | |||||||||
Keywords | OUTER MEMBRANE PROTEIN / PORIN | |||||||||
Function / homology | Function and homology information polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / monoatomic ion transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å | |||||||||
Authors | Diederichs, K. / Welte, W. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Authors: Forst, D. / Welte, W. / Wacker, T. / Diederichs, K. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Scry, a Specific Bacterial Outer Membrane Porin Authors: Forst, D. / Schulein, K. / Wacker, T. / Diederichs, K. / Kreutz, W. / Benz, R. / Welte, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0t.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0t.ent.gz | 204.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a0t_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1a0t_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 1a0t_validation.xml.gz | 50 KB | Display | |
Data in CIF | 1a0t_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0t ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0t | HTTPS FTP |
-Related structure data
Related structure data | 1a0sC 1aosS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 45333.668 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: OUTER MEMBRANE / Gene: SCRY / Plasmid: PSO112 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): KS 26 / References: UniProt: P22340 #2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #3: Chemical | #4: 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: 3.8 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.7 Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D- ...Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D-OCTYLGLUCOPYRANOSIDE AND 6-9% PEG-2000. THE CONCENTRATION OF PEG IN THE RESERVOIR WAS 12-15%. 2M SUCROSE WAS ADDED TO THE DROP FOR COCRYSTALLIZATION., vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Type: OTHER / Wavelength: 1.5418 |
Detector | Type: STOE / Detector: DIFFRACTOMETER / Date: Apr 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→17 Å / Num. obs: 65815 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 2.74 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.155 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.4→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.524 / % possible all: 84 |
Reflection | *PLUS Rmerge(I) obs: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: SUCROSE PORIN (PDB ENTRY 1AOS) Resolution: 2.4→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.1 Å / Weight Biso : 1 / Weight position: 50
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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