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Record for CD0000101000 (Bacteriorhodopsin)

Download the PCDDB data file for this record

Sample

PCDDBIDCD0000101000
Protein NameBacteriorhodopsin
Alternative Protein NamesBR
Source OrganismHalobacterium salinarum
Protein SupplierP.Booth, Bristol
Expression System or natural sourcenatural source
Expressed AsWild-type
Mutation DetailsNo data provided
Expression tags (if any)No data provided
Ligands Present and Concentration or ratioNo data provided
Macromolecular Partner(s) and Concentration or ratioNo data provided
Deposition Date2011-08-19

Spectra

PCDDBIDCD0000101000
Raw Sample SpectraNo data provided
Dichroism Units of Raw Sample DataNo data provided
HT / High Voltage / Dynode Spectra file   chart
Raw Baseline SpectraNo data provided
Dichroism Units of Raw Baseline DataNo data provided
Average SampleNo data provided
Dichroism Units of Average Sample DataNo data provided
Averaged BaselineNo data provided
Dichroism Units of Averaged Baseline DataNo data provided
Net Smoothed Spectrum file   chart
Dichroism Units of Net Smoothed DataDRS units
Final Processed Spectrum file   chart
Dichroism Units of Processed DataDelta Epsilon

Experiment

PCDDBIDCD0000101000
CD or SRCDSRCD
Protein Concentration (mg/ml)3.37
Concentration Quantification MethodExtinction Coefficient
Protein Purity (%)No data provided
Purity Quantification MethodNo data provided
Buffer Contents and Concentrations1.2% OG
Baseline Contents1.2% OG
Experimental Temperature (C)4
Instrument or beamlineDaresbury 3.1
Detector Angle (Scattering Angle)No data provided
Sample Cell Pathlength (cm)0.0013
Cell Pathlength Calibration MethodInterferometry
Sample Cell TypeCylindrical-Demountable
Sample Cell CompositionSuprasil
Sample Chamber AtmosphereNitrogen
Number of repeat scans2
Continuous or Stepped scanStepped
Maximum (highest) wavelength, nm280
Minimum (lowest) wavelength, nm173
Criteria for low wavelength cutoffHT value
Wavelength interval, nm0.2
Dwell or Averaging time, seconds3
Experimental Collection date2003-05-13
Local Spectrum Identifiert16122

Calibration

PCDDBIDCD0000101000
CSA or ACSCSA
CSA/ACS Standard Spectrum file   chart
Dichroism Units for CSA StandardDRS units
Final Spectrum CalibratedYES
CSA/ACS Standard Concentration (mg/ml)9.80
CSA/ACS Pathlength (mm)0.10
CSA/ACS Zeroed at-
CSA/ACS Date Measured2003-05-13
CSA/ACS Ratio (192.5nm and 290.0 nm)2.12
CD signal at 290nm (mdeg)348781
CSA/ACS Experiment temperature, C25

Data Process

PCDDBIDCD0000101000
Molecular Weight26915.6
Number of Residues249
Mean Residue Weight108.5
Data Processing Software NameCDTool
Data Processing Software Version1.4
Number of Smoothing Points7
Wavelength Range for Zeroing263-270

Sec. Struct.

PCDDBIDCD0000101000
Secondary Structure Calculated fromCrystal structure
DSSP value: alpha helix0.685
DSSP value: 3-10 helix0.012
DSSP value: pi helix0.000
DSSP value: beta strand0.048
DSSP value: beta bridge0.000
DSSP value: bonded turn0.085
DSSP value: bend0.032
DSSP value: loop or irregular0.137

Info.

PCDDBIDCD0000101000
PDB ID1qhj: RSCBpdb PDBj PDBe
UniProt IDP02945
Enzyme Classification (EC)-
Medline Entry21505036 (pubmed)
Cath Classification1.20.1070.10
SequenceQAQITGRPEW IWLALGTALM GLGTLYFLVK GMGVSDPDAK KFYAITTLVP AIAFTMYLSM LLGYGLTMVP FGGEQNPIYW ARYADWLFTT PLLLLDLALL VDADQGTILA LVGADGIMIG TGLVGALTKV YSYRFVWWAI STAAMLYILY VLFFGFTSKA ESMRPEVAST FKVLRNVTVV LWSAYPVVWL IGSEGAGIVP LNIETLLFMV LDVSAKVGFG LILLRSRAIF GEAEAPEPSA GDGAAATSD
Type of proteinmembrane
Keyword/phrase AMP180
Keyword/phrase BSMP180
Keyword/phrase Cmembrane protein
Keyword/phrase DNo data provided
Keyword/phrase ENo data provided
Keyword/phrase FNo data provided
Keyword/phrase GNo data provided
Keyword/phrase HNo data provided
Keyword/phrase INo data provided
Keyword/phrase JNo data provided
Publication AuthorsAli Abdul-Gader, Andrew John Miles and B.A. Wallace
Publication Year2011
Publication JournalBioinformatics
Publication TitleA Reference Dataset for the Analyses of Membrane Protein Sec-ondary Structures and Transmembrane Residues using Circular Dichroism Spectroscopy
Publication Volume27
Publication Pages1630-1636
Citation PublicationNo data provided

Depositor

PCDDBIDCD0000101000
Depositor NameAndrew Miles
Department/School namecrystallography
University/Institution/CorporationBirkbeck
Depositor CountryUnited Kingdom
Name of Principal Investigator (if not depositor)BA Wallace

Validation

PCDDBID CD0000101000
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 PASS
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 INSUFFICIENT DATA
Standard Deviation INSUFFICIENT DATA
Noise: 260-270nm PASS
Flat topped peaks PASS
Wavelength range PASS
Interval resolution PASS
High Tension Voltage 240-260nm PASS
Projection Test FLAG
Standard Deviation At Peak INSUFFICIENT DATA
Overall validation level is: FLAG
Validation report compiled by Validichro v1.2.5, 2011-08-19, 10:26am.
Depositor comment for validation report : Standard deviation and Standard deviation at peak: test cannot be carried out because no raw data available. projection test: flagged because it is an unusual spectrum
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