SASDCC6: Sensory box domain of the sensory-box/GGDEF protein SO_1695 from ...

Basic information

• Entry: Database: SASBDB / ID: SASDCC6

Sample

Sensory box domain of the sensory-box/GGDEF protein SO_1695 from Shewanella oneidensis, Northeast Structural Genomics Consortium Target SoR288B

• Diguanylate cyclase with PAS sensory domain (protein), Shewanella oneidensis (strain MR-1)

Function / homology

Function:

negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / plasma membrane

Domain/homology:

: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS domain / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain

Component:

diguanylate cyclase

• Biological species: Shewanella oneidensis (strain MR-1) (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 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.

Models

• Model #1412: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 4.756761; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1413: ; Type: dummy / Radius of dummy atoms: 1.75 A / Chi-square value: 2.039184; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Sensory box domain of the sensory-box/GGDEF protein SO_1695 from Shewanella oneidensis, Northeast Structural Genomics Consortium Target SoR288B; Specimen concentration: 3.90-12.30
• Buffer: Name: 5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3 / pH: 7.5

Entity #747

Type: protein / Description: Diguanylate cyclase with PAS sensory domain / Formula weight: 14.722 / Num. of mol.: 2 / Source: Shewanella oneidensis (strain MR-1) / References: UniProt: Q8EGB0
Sequence:

MEHSSLETIE LFIQHLTEAM ILVNANGFIR SCNQRSAELL DCPQVSLKGQ DWRNFLTEHH QARYDNLLSH DVQLGTNCGQ PVQHPAQETT LICASGKAKD VELSISYIPG HEPMFVMVMH DLEHHHHHH

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: Sensory box domain of the sensory-box/GGDEF protein SO_1695 from Shewanella oneidensis, Northeast Structural Genomics Consortium Target SoR288B
Measurement date: Feb 12, 2010 / Storage temperature: -80 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /

	Min	Max
Q	0.0213	0.3492

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 386 /

	Min	Max
Q	0.03975	0.3492
P(R) point	23	408
R	0	64.23

Result

D max: 6.42 / Type of curve: single_conc /

	Experimental	Porod
MW	28.83 kDa	28.83 kDa
Volume	-	47.86 nm3

	P(R)	Guinier
Forward scattering, I0	830.5	823.82
Radius of gyration, Rg	1.96 nm	1.96 nm