[English] 日本語
Yorodumi- SASDCG6: EAL/GGDEF domain protein from M. capsulatus, Northeast Structural... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDCG6 |
---|---|
Sample | EAL/GGDEF domain protein from M. capsulatus, Northeast Structural Genomics Consortium Target McR174C
|
Function / homology | Function and homology information Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain Similarity search - Domain/homology |
Biological species | Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (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 |
---|
-Downloads & links
-Data source
SASBDB page | SASDCG6 |
---|
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-External links
Related items in Molecule of the Month |
---|
-Models
Model #1433 | Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 13.653025 Search similar-shape structures of this assembly by Omokage search (details) |
---|---|
Model #1434 | Type: dummy / Radius of dummy atoms: 2.00 A / Chi-square value: 1.996569 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: EAL/GGDEF domain protein from M. capsulatus, Northeast Structural Genomics Consortium Target McR174C Specimen concentration: 2.82-5.07 |
---|---|
Buffer | Name: 5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3 / pH: 7.5 |
Entity #751 | Type: protein / Description: EAL/GGDEF domain protein / Formula weight: 18.775 / Num. of mol.: 1 Source: Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) References: UniProt: Q60BX6 Sequence: MDTVTGLPNR QLFCDRLLQA LAAHERDGNP VVLLFLDVDN FKSINDSLGH LVGDRLLRAT AERIRTAVRD GDTVARIGGD EFTILLNGAK DTLNGALVAQ KILDGLAQPF VFGAQQIVIS VSIGIAVSPA DGETMEQLLR NADTAMYHAK SRGKNNYQFF SPELEHHHHH 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 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: Rayonix MX225-HE | ||||||||||||||||||
Scan | Title: EAL/GGDEF domain protein from M. capsulatus, Northeast Structural Genomics Consortium Target McR174C Measurement date: Feb 12, 2010 / Storage temperature: -80 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /
| ||||||||||||||||||
Distance distribution function P(R) | Sofotware P(R): GNOM 4.5a / Number of points: 330 /
| ||||||||||||||||||
Result | D max: 6.55 / Type of curve: single_conc /
|