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Yorodumi- SASDCD6: MucBP domain of the adhesion protein PEPE_0118 from Pediococcus p... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDCD6 |
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Sample | MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A
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Function / homology | Mub B2-like domain / Muc B2-like domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Adhesion exoprotein Function and homology information |
Biological species | Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w) (bacteria) |
Citation | Journal: Biopolymers / Year: 2011 Title: Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Authors: Thomas D Grant / Joseph R Luft / Jennifer R Wolfley / Hiro Tsuruta / Anne Martel / Gaetano T Montelione / Edward H Snell / Abstract: Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained ...Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDCD6 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #1421 | Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 37.540129 Search similar-shape structures of this assembly by Omokage search (details) |
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Model #1422 | Type: dummy / Radius of dummy atoms: 2.00 A / Chi-square value: 7.963684 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A Specimen concentration: 2.53-7.67 |
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Buffer | Name: 5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3 / pH: 7.5 |
Entity #748 | Type: protein / Description: Adhesion exoprotein / Formula weight: 14.384 / Num. of mol.: 1 Source: Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w) References: UniProt: Q03HU7 Sequence: MPNYDATHAT STETIHYVNE DGDQVFEDGG GKLDFTRTVT IDDVTNEVVE YGEWTPVTDD EFAAVTSPDK DGYTPDTSEV AAQKPDMTDG PDGTVKDVEV TVTYTANPAV ATITYVDDDE NGKLEHHHHH H |
-Experimental information
Beam | Instrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2 City: Stanford, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.13 Å / Dist. spec. to detc.: 1.5 mm | ||||||||||||||||||
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Detector | Name: Rayonix MX225-HE | ||||||||||||||||||
Scan | Title: MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A Measurement date: Feb 12, 2010 / Storage temperature: -80 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 4.5a / Number of points: 401 /
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Result | D max: 8.2 / Type of curve: single_conc /
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