Phosphoglycerate Kinase (pgk1)

Citation: Lees, J.G., Wien, F., Miles, A.J. & Wallace, B.A., 2006 Bioinformatics 22 1955-1962

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	DRS units	Download	View Plot
Raw Sample Spectra	Daresbury Arbitrary Units	Download	View Plot
Raw Sample Spectra 2	Daresbury Arbitrary Units	Download	View Plot
Raw Sample Spectra 3	Daresbury Arbitrary Units	Download	View Plot
Raw Baseline Spectra	Daresbury Arbitrary Units	Download	View Plot
Raw Baseline Spectra 2	Daresbury Arbitrary Units	Download	View Plot
Raw Baseline Spectra 3	Daresbury Arbitrary Units	Download	View Plot
Average Sample	Daresbury Arbitrary Units	Download	View Plot
Averaged Baseline	Daresbury Arbitrary Units	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
Net Smoothed Spectrum	Daresbury Arbitrary Units	Download	View Plot
Final Processed Spectrum	Delta Epsilon	Download	View Plot

Validation report compiled by Validichro v1.0, 2009-12-15, 13:00. - PASS

At a glance

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Sample

Protein Name	Phosphoglycerate kinase	?
Alternative Protein Names	PGK1	?
Source Organism	S. cerevisiae	?
Protein Supplier	No data provided	?
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	2009-11-28	?

Experiment

CD or SRCD	SRCD	?
Protein Concentration (mg/ml)	5.65	?
Concentration Quantification Method	QAA	?
Protein Purity (%)	No data provided	?
Purity Quantification Method	No data provided	?
Buffer Contents and Concentrations	water	?
Baseline Contents	water	?
Experimental Temperature (C)	4	?
Instrument or beamline	Daresbury 12.1	?
Detector Angle (Scattering Angle)	No data provided	?
Sample Cell Pathlength (cm)	0.0015	?
Cell Pathlength Calibration Method	Interferometry	?
Sample Cell Type	Cylindrical-Demountable	?
Sample Cell Composition	Suprasil	?
Sample Chamber Atmosphere	Nitrogen	?
Number of repeat scans	3	?
Continuous or Stepped scan	No data provided	?
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	1	?
Experimental Collection date	2004-02-03	?
Local Spectrum Identifier	r7958	?

Calibration

CSA or ACS	CSA	?
Dichroism Units for CSA Standard	DRS units	?
Final Spectrum Calibrated	No data provided	?
CSA/ACS Standard Concentration (mg/ml)	9.35	?
CSA/ACS Pathlength (mm)	0.1	?
CSA/ACS Zeroed at	No data provided	?
CSA/ACS Date Measured	2004-02-03	?
CSA/ACS Ratio (192.5nm and 290.0 nm)	2.28	?
CD signal at 290nm (mdeg)	No data provided	?
CSA/ACS Experiment temperature, C	25	?

Data process.

Molecular Weight	44608	?
Number of Residues	415	?
Mean Residue Weight	107.7	?
Data Processing Software Name	CDTool	?
Data Processing Software Version	1.4	?
Wavelength Range for Zeroing	263-267	?
Number of Smoothing Points	5	?

Sec. struct.

Secondary Structure Calculated from	PDB File	?
DSSP value: alpha helix	0.345	?
DSSP value: 3-10 helix	0.000	?
DSSP value: pi helix	0.000	?
DSSP value: beta strand	0.111	?
DSSP value: beta bridge	0.005	?
DSSP value: bonded turn	0.041	?
DSSP value: bend	0.229	?
DSSP value: loop or irregular	0.270	?

Tertiary

PDB ID	3pgk	?
UniProt ID	P00560	?
Enzyme Classification (EC)	2.7.2.3	?
Medline Entry	16787970	?
Cath Classification	3.40.50.1260 3.40.50.1270	?
Sequence	SLSSKLSVQD LDLKDKRVFI RVDFNVPLDG KKITSNQRIV AALPTIKYVL EHHPRYVVLA SHLGRPNGER NEKYSLAPVA KELQSLLGKD VTFLNDCVGP EVEAAVKASA PGSVILLENL RYHIEEEGSR KVDGQKVKAS KEDVQKFRHE LSSLADVYIN DAFGTAHRAH SSMVGFDLPQ RAAGFLLEKE LKYFGKALEN PTRPFLAILG GAKVADKIQL IDNLLDKVDS IIIGGGMAFT FKKVLENTEI GDSIFDKAGA EIVPKLMEKA KAKGVEVVLP VDFIIADAFS ADANTKTVTD KEGIPAGWQG LDNGPESRKL FAATVAKAKT IVWNGPPGVF EFEKFAAGTK ALLDEVVKSS AAGNTVIIGG GDTATVAKKY GVTDKISHVS TGGGASLELL EGKELPGVAF LSEKK	?
Type of protein	soluble globular	?
Keyword/phrase A	SP175	?
Keyword/phrase B	multi domain type	?
Keyword/phrase C	mixed alpha 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	Lees, J.G., Wien, F., Miles, A.J. & Wallace, B.A.,	?
Publication Year	2006	?
Publication Journal	Bioinformatics	?
Publication Title	A reference database for circular dichroism spectroscopy covering fold and secondary structure space	?
Publication Volume	22	?
Publication Pages	1955-1962	?

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 v1.0, 2009-12-15, 13:00. - PASS

Depositors Notes: NULL

Maximum Delta Epsilon	PASS	?
Minimal Level of Maximum Delta Epsilon	PASS	?
Signal to noise ratio	PASS	?
Deviations from zero	PASS	?
High Tension Voltage readings	PASS	?
Wavelength range covered (low end / high end)	PASS PASS	?
Interval resolution	PASS	?
Deviation between 260-270nm	PASS	?
Mean Residue Weight value	PASS	?
Flat topped peaks	PASS	?
CSA or ACS standard used	PASS	?
Width of peaks at half height	PASS	?
Peak and trough locations	PASS	?
Spectral Feature Width	PASS	?
CSA / ACS peak ratio	PASS	?
Calibration data at 290nm	N/A	?
Sum of DSSP fractions	PASS	?
Depositor Note		?