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- PDB-1r2n: NMR structure of the all-trans retinal in dark-adapted Bacteriorh... -

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Basic information

Entry
Database: PDB / ID: 1r2n
TitleNMR structure of the all-trans retinal in dark-adapted Bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / PROTON PUMP / RETINAL PROTEIN / PHOTOreceptor / HALOARCHAEA / proton transport
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / 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 / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarium (Halophile)
MethodSOLUTION NMR / simulated annealing
AuthorsPatzelt, H. / Simon, B. / terLaak, A. / Kessler, B. / Kuhne, R. / Schmieder, P. / Oesterhaelt, D. / Oschkinat, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy
Authors: Patzelt, H. / Simon, B. / terLaak, A. / Kessler, B. / Kuhne, R. / Schmieder, P. / Oesterhaelt, D. / Oschkinat, H.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2142
Polymers26,9301
Non-polymers2841
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100rms distance between observed and calculated chemical shifts
RepresentativeModel #1lowest energy

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 26929.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purple membrane / Source: (natural) Halobacterium salinarium (Halophile) / Strain: R1 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
3312D NOESY

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Sample preparation

DetailsContents: residue specifically labeled purple membrane (12-20 mg Bacteriorhodopsin) suspended in 1% deuterated dodecal maltoside, 10 mM potassium phosphate buffer in D2O
Solvent system: D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11 6.5 1 atm308 K
21 6.5 1 atm313 K
31 6.5 1 atm318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX8001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker, A.G.processing
Amber4.1Kollman, P.structure solution
Amber4.1Kollman, P.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NMR structures of the active center in dark-adapted bacteriorhodopsin were calculated using PDB entry 1BRR, as a template, and 32 NOE restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: rms distance between observed and calculated chemical shifts
Conformers calculated total number: 100 / Conformers submitted total number: 12

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