Avidin

Citation: Miles, A.J,, Whitmore, L.,Janes, R.W. & Wallace, B.A. 2014 Scientific data

Citation: The PCDDB (protein circular dichroism data bank): A bioinformatics resource for protein characterisations and methods development.
Ramalli SG, Miles AJ, Janes RW, Wallace BA., J Mol Biol (2022)

CSA/ACS Standard Spectrum	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra 2	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra 3	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra 4	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra 5	Millidegrees (theta)	Download	View Plot
Raw Sample Spectra 6	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra 2	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra 3	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra 4	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra 5	Millidegrees (theta)	Download	View Plot
Raw Baseline Spectra 6	Millidegrees (theta)	Download	View Plot
Average Sample	Millidegrees (theta)	Download	View Plot
Averaged Baseline	Millidegrees (theta)	Download	View Plot
HT / High Voltage / Dynode Spectra	HT/Dynode Units	Download	View Plot
HT / High Voltage / Dynode Spectra 2	HT/Dynode Units	Download	View Plot
HT / High Voltage / Dynode Spectra 3	HT/Dynode Units	Download	View Plot
HT / High Voltage / Dynode Spectra 4	HT/Dynode Units	Download	View Plot
HT / High Voltage / Dynode Spectra 5	HT/Dynode Units	Download	View Plot
HT / High Voltage / Dynode Spectra 6	HT/Dynode Units	Download	View Plot
Net Smoothed Spectrum	Millidegrees (theta)	Download	View Plot
Final Processed Spectrum	Delta Epsilon	Download	View Plot

Validation report compiled by Validichro v1.4.0.1, 2022-09-27 10:26:54. - PASS

At a glance

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Sample

Protein Name	Avidin	?
Alternative Protein Names	No data provided	?
Source Organism	gallus gallus	?
Protein Supplier	Sigma Aldrich	?
Expression System or natural source	natural source	?
Expressed As	Wild-type	?
Mutation Details	No data provided	?
Expression tags (if any)	No data provided	?
Ligands Present and Concentration or ratio	No data provided	?
Macromolecular Partner(s) and Concentration or ratio	No data provided	?
Deposition Date	2014-03-26	?

Experiment

CD or SRCD	SRCD	?
Protein Concentration (mg/ml)	2.8	?
Concentration Quantification Method	QAA	?
Protein Purity (%)	>95	?
Purity Quantification Method	SDS gels	?
Buffer Contents and Concentrations	H2O	?
Baseline Contents	H2O	?
Experimental Temperature (C)	4	?
Instrument or beamline	ISA CD1	?
Detector Angle (Scattering Angle)	No data provided	?
Sample Cell Pathlength (cm)	0.0024	?
Cell Pathlength Calibration Method	Interferometry	?
Sample Cell Type	Cylindrical-Demountable	?
Sample Cell Composition	Suprasil	?
Sample Chamber Atmosphere	Nitrogen	?
Number of repeat scans	4	?
Continuous or Stepped scan	Stepped	?
Maximum (highest) wavelength, nm	280	?
Minimum (lowest) wavelength, nm	175	?
Criteria for low wavelength cutoff	HT value	?
Wavelength interval, nm	1	?
Dwell or Averaging time, seconds	2	?
Experimental Collection date	2011-03-12	?
Local Spectrum Identifier	A21818	?

Calibration

CSA or ACS	CSA	?
Dichroism Units for CSA Standard	Millidegrees (theta)	?
Final Spectrum Calibrated	YES	?
CSA/ACS Standard Concentration (mg/ml)	5.84	?
CSA/ACS Pathlength (mm)	0.1	?
CSA/ACS Zeroed at	235-245	?
CSA/ACS Date Measured	2011-03-12	?
CSA/ACS Ratio (192.5nm and 290.0 nm)	2.05	?
CD signal at 290nm (mdeg)	20.06	?
CSA/ACS Experiment temperature, C	25	?

Data process.

Molecular Weight	14344	?
Number of Residues	128	?
Mean Residue Weight	112.9	?
Data Processing Software Name	CDTool	?
Data Processing Software Version	1.4	?
Wavelength Range for Zeroing	263-270	?
Number of Smoothing Points	7	?

Sec. struct.

Secondary Structure Calculated from	PDB file	?
DSSP value: alpha helix	0.000	?
DSSP value: 3-10 helix	0.066	?
DSSP value: pi helix	0.000	?
DSSP value: beta strand	0.45.6	?
DSSP value: beta bridge	0.000	?
DSSP value: bonded turn	0.015	?
DSSP value: bend	0.147	?
DSSP value: loop or irregular	0.316	?

Tertiary

PDB ID	1rav	?
UniProt ID	P02701	?
Enzyme Classification (EC)	No data provided	?
Medline Entry	No data provided	?
Cath Classification	2.40.128.30	?
Sequence	ARKCSLTGKW TNDLGSNMTI GAVNSRGEFT GTYITAVTAT SNEIKESPLH GTQNTINKRT QPTFGFTVNW KFSESTTVFT GQCFIDRNGK EVLKTMWLLR SSVNDIGDDW KATRVGINIF TRLRTQKE	?
Type of protein	soluble globular	?
Keyword/phrase A	SP175a	?
Keyword/phrase B	single domain type	?
Keyword/phrase C	beta	?
Keyword/phrase D	No data provided	?
Keyword/phrase E	No data provided	?
Keyword/phrase F	No data provided	?
Keyword/phrase G	No data provided	?
Keyword/phrase H	No data provided	?
Keyword/phrase I	No data provided	?
Keyword/phrase J	No data provided	?
Publication Authors	Miles, A.J,, Whitmore, L.,Janes, R.W. & Wallace, B.A.	?
Publication Year	2014	?
Publication Journal	Scientific data	?
Publication Title	A "Gold Standard" Reference Dataset for Protein Circular Dichroism Spectral and Meta-Data	?
Publication Volume	No data provided	?
Publication Pages	No data provided	?

Depositor

Depositor Name	Andrew Miles	?
Department/School name	crystallography	?
University/Institution/Corporation	Birkbeck	?
Depositor Country	United Kingdom	?
Name of Principal Investigator (if not depositor)	B.A. Wallace	?

Validation report compiled by Validichro v1.4.0.1, 2022-09-27 10:26:54. - PASS

Depositors Notes:

Missing Wavelengths	PASS	?
Maximum Delta Epsilon	PASS	?
Minimal Level of Maximum Delta Epsilon	PASS	?
Peak Locations	PASS	?
Feature Width	PASS	?
Experimental Temperature	PASS	?
UniProt sequence		?
Molecular Weight	PASS	?
Number of Residues	PASS	?
Mean Residue Weight value	PASS	?
Concentration and Pathlength	PASS	?
CSA / ACS peak ratio	PASS	?
CSA / ACS Temperature	PASS	?
Peak Shift test	PASS	?
Standard Deviation	PASS	?
Noise: 260-270nm	PASS	?
Flat topped peaks	PASS	?
Wavelength range	PASS	?
Interval resolution	PASS	?
High Tension Voltage 240-260nm	PASS	?
Projection Test	PASS	?
Standard Deviation At Peak	PASS	?
Depositor Note		?