SASDCQ2: 4Ca2+-calmodulin - Xenopus laevis (Calmodulin, CaM)

Basic information

• Entry: Database: SASBDB / ID: SASDCQ2

Sample

4Ca2+-calmodulin - Xenopus laevis

• Calmodulin (protein), CaM, Xenopus laevis

Function / homology

Function:

signaling receptor binding / calcium ion binding

Domain/homology:

EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair

Component:

Calmodulin-2 B

• Biological species: Xenopus laevis (African clawed frog)
• Citation: Journal: Acta Crystallogr D Struct Biol / Year: 2017; Title: 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.; Authors: Jill Trewhella / Anthony P Duff / Dominique Durand / Frank Gabel / J Mitchell Guss / Wayne A Hendrickson / Greg L Hura / David A Jacques / Nigel M Kirby / Ann H Kwan / Javier Pérez / Lois Pollack / Timothy M Ryan / Andrej Sali / Dina Schneidman-Duhovny / Torsten Schwede / Dmitri I Svergun / Masaaki Sugiyama / John A Tainer / Patrice Vachette / John Westbrook / Andrew E Whitten / ; Abstract: In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

Contact author

• Jill Trewhella (School of Molecular Bioscience, University of Sydney., Sydney, New South Wales 2006, Australia)

Models

• Model #1176: ; Type: dummy / Software: (on-line) / Radius of dummy atoms: 1.80 A / Symmetry: P1 / Chi-square value: 0.844 / P-value: 0.532600; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1177: ; Type: atomic / Software: (on-line) / Radius of dummy atoms: 1.90 A / Symmetry: P1; Comment: Representative model from 1-state ensemble calculation, flexible residues 77-81; Chi-square value: 0.840129176626 / P-value: 0.314400; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1178: ; Type: atomic / Software: (on-line) / Radius of dummy atoms: 1.90 A / Symmetry: P1; Comment: Representative model-0 from 2-state ensemble, flexible residues 77-81; Chi-square value: 0.790816234359 / P-value: 0.787700; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1179: ; Type: atomic / Software: (on-line) / Radius of dummy atoms: 1.90 A / Symmetry: P1; Comment: Representative model-1 from 2-state ensemble, flexible residues 77-81; Chi-square value: 0.790816234359 / P-value: 0.787700; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: 4Ca2+-calmodulin - Xenopus laevis / Specimen concentration: 0.74-1.10
• Buffer: Name: 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3; pH: 7.5 ; Comment: 2 mM TCEP and 0.1% (.01538 M) NaN3 used for radiation protection

Entity #614

Name: CaM / Type: protein / Description: Calmodulin / Formula weight: 16.706 / Num. of mol.: 1 / Source: Xenopus laevis / References: UniProt: P62155
Sequence:

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 2.683 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: 4Ca2+-calmodulin - Xenopus laevis / Measurement date: Mar 9, 2017 / Cell temperature: 22 °C / Exposure time: 1 sec. / Number of frames: 24 / Unit: 1/A /

	Min	Max
Q	0.0066	0.3104

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 390 /

	Min	Max
Q	0.00740724	0.310411
P(R) point	1	390
R	0	72.2

Result

Type of curve: other

	Experimental	Standard	Porod
MW	16.842 kDa	22.003 kDa	16.8 kDa
Volume	-	-	25.2 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.02667	0.0003	0.027	2.5E-5
Radius of gyration, Rg	2.219 nm	0.003	2.174 nm	0.006

	Min	Max
D	-	7.22
Guinier point	2	69