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- PDB-1jv7: BACTERIORHODOPSIN O-LIKE INTERMEDIATE STATE OF THE D85S MUTANT AT... -

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Basic information

Entry
Database: PDB / ID: 1jv7
TitleBACTERIORHODOPSIN O-LIKE INTERMEDIATE STATE OF THE D85S MUTANT AT 2.25 ANGSTROM RESOLUTION
ComponentsBacteriorhodopsin
KeywordsION TRANSPORT / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / D85S MUTANT / O-LIKE STATE / PHOTOCYCLE INTERMEDIATE / CUBIC LIPID PHASE
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / proton transmembrane transport / 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
Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRouhani, S. / Cartailler, J.-P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate.
Authors: Rouhani, S. / Cartailler, J.P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,93811
Polymers26,9011
Non-polymers6,03710
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.800, 121.300, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bacteriorhodopsin / BR


Mass: 26901.490 Da / Num. of mol.: 1 / Mutation: D85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: Bop / Plasmid: pNov-r / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: cubic lipid phase / pH: 5.6
Details: monoolein, octyl-beta-D-glucopyranoside, pH 5.6, cubic lipid phase, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 Msodium potassium Pi11
23.5 mg/mlprotein11
30.05 %methylpentandiol11
41.2 %beta-octylglycopyranoside11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Oct 16, 1998
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 12730 / Num. obs: 11949 / % possible obs: 91.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 13 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.6
Reflection shellResolution: 2.25→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / Num. unique all: 646 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 164767
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRX

1brx


Resolution: 2.25→12 Å / Isotropic thermal model: isotropic / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 535 5 %random
Rwork0.213 ---
all0.25 13069 --
obs0.216 10213 --
Refinement stepCycle: LAST / Resolution: 2.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 161 33 1823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0082
X-RAY DIFFRACTIONc_angle_deg1.108
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0082

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