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- PDB-2ksy: Solution nmr structure of sensory rhodopsin II -

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Basic information

Entry
Database: PDB / ID: 2ksy
TitleSolution nmr structure of sensory rhodopsin II
ComponentsSensory rhodopsin II
KeywordsMEMBRANE PROTEIN / membrane proteins / NMR spectroscopy / receptors / structure elucidation / transmembrane
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / RETINAL / :
Function and homology information
Biological speciesNatronomonas pharaonis (archaea)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsGautier, A. / Mott, H.R. / Bostock, M.J. / Kirkpatrick, J.P. / Nietlispach, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.
Authors: Gautier, A. / Mott, H.R. / Bostock, M.J. / Kirkpatrick, J.P. / Nietlispach, D.
History
DepositionJan 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 10, 2015Group: Non-polymer description / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory rhodopsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7402
Polymers26,4561
Non-polymers2841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sensory rhodopsin II


Mass: 26455.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IMZ8
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
Nonpolymer detailsLIGAND LYR IS LYSINE_RETINAL

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1333D HNCA
1433D HN(CO)CA
1533D HNCO
1633D HN(CA)CO
1733D HN(CA)CB
1833D HN(COCA)CB
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] SENSORY RHODOPSIN II-1, 50 mM sodium chloride-2, 50 mM sodium phosphate-3, 0.05 % sodium azide-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] SENSORY RHODOPSIN II-5, 50 mM sodium chloride-6, 50 mM sodium phosphate-7, 0.05 % sodium azide-8, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N; U-2H] SENSORY RHODOPSIN II-9, 50 mM sodium chloride-10, 50 mM sodium phosphate-11, 0.05 % sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSENSORY RHODOPSIN II-1[U-100% 15N]1
50 mMsodium chloride-21
50 mMsodium phosphate-31
0.05 %sodium azide-41
0.5 mMSENSORY RHODOPSIN II-5[U-100% 13C; U-100% 15N]2
50 mMsodium chloride-62
50 mMsodium phosphate-72
0.05 %sodium azide-82
0.5 mMSENSORY RHODOPSIN II-9[U-13C; U-15N; U-2H]3
50 mMsodium chloride-103
50 mMsodium phosphate-113
0.05 %sodium azide-123
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CcpNmr_AnalysisCCPNchemical shift assignment
CcpNmr_AnalysisCCPNchemical shift calculation
CcpNmr_AnalysisCCPNpeak picking
AZARABoucherprocessing
TALOSCornilescu, Delaglio and Baxtorsion angle prediction
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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