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- PDB-2l6x: Solution NMR Structure of Proteorhodopsin. -

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Basic information

Entry
Database: PDB / ID: 2l6x
TitleSolution NMR Structure of Proteorhodopsin.
ComponentsGreen-light absorbing proteorhodopsin
KeywordsPROTON TRANSPORT / proteorhodopsin / membrane protein structure / cell-free expression / Structural Genomics / PSI:Biology / Protein Structure Initiative / Membrane Protein Structures by Solution NMR / MPSbyNMR
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Proteorhodopsin / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINAL / Green-light absorbing proteorhodopsin
Similarity search - Component
Biological speciesuncultured marine gamma proteobacterium EBAC31A08 (environmental samples)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsReckel, S. / Gottstein, D. / Stehle, J. / Loehr, F. / Takeda, M. / Silvers, R. / Kainosho, M. / Glaubitz, C. / Bernhard, F. / Schwalbe, H. ...Reckel, S. / Gottstein, D. / Stehle, J. / Loehr, F. / Takeda, M. / Silvers, R. / Kainosho, M. / Glaubitz, C. / Bernhard, F. / Schwalbe, H. / Guntert, P. / Doetsch, V. / Membrane Protein Structures by Solution NMR (MPSbyNMR)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Solution NMR structure of proteorhodopsin.
Authors: Reckel, S. / Gottstein, D. / Stehle, J. / Lohr, F. / Verhoefen, M.K. / Takeda, M. / Silvers, R. / Kainosho, M. / Glaubitz, C. / Wachtveitl, J. / Bernhard, F. / Schwalbe, H. / Guntert, P. / Dotsch, V.
History
DepositionNov 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Apr 11, 2012Group: Other
Revision 1.3Jun 17, 2015Group: Non-polymer description
Revision 1.4Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green-light absorbing proteorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0092
Polymers26,7251
Non-polymers2841
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Green-light absorbing proteorhodopsin / GPR


Mass: 26724.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine gamma proteobacterium EBAC31A08 (environmental samples)
Strain: EBAC31A08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F7P4
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1323D HNCA
1423D HN(CA)CB
1523D HNCO
1613D HCACO
1733D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-13C; U-15N] proteorhodopsin, 90% H2O/10% D2O90% H2O/10% D2O
2300 uM [U-13C; U-15N; U-2H] proteorhodopsin, 90% H2O/10% D2O90% H2O/10% D2O
3300 uM [U-15N; U-2H] proteorhodopsin, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMproteorhodopsin-1[U-13C; U-15N]1
300 uMproteorhodopsin-2[U-13C; U-15N; U-2H]2
300 uMproteorhodopsin-3[U-15N; U-2H]3
Sample conditionsIonic strength: 0.025 / pH: 5 / Pressure: AMBIENT / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003
Bruker AvanceBrukerAVANCE9504

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
SparkyGoddardchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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