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- PDB-6rmk: Bacteriorhodopsin, dark state, cell 2, refined using the same pro... -

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Basic information

Entry
Database: PDB / ID: 6rmk
TitleBacteriorhodopsin, dark state, cell 2, refined using the same protocol as sub-ps time delays
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump / time-resolved crystallography / free-electron laser
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 salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. ...Nass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2019
Title: Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.
Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / ...Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J.E. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Heyne, K. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,5882
Polymers25,3041
Non-polymers2841
Water64936
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7656
Polymers75,9123
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6420 Å2
ΔGint-52 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 62.100, 110.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 25303.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 / Variant: ATCC 700922 / JCM 11081 / NRC-1 / 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.: 36 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 32% (W/V) PEG 2000, 0.1 M K2HPO4 /NAH2PO4, IN HAMILTON SYRINGES, PH 5.6, LIPIDIC CUBIC PHASE,

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.26 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.8→20.444 Å / Num. obs: 22403 / % possible obs: 100 % / Redundancy: 476 % / R split: 0.154 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 1140

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6V

5b6v


Resolution: 1.8→20.441 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2492 1137 5.08 %
Rwork0.2435 --
obs0.2439 22360 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 20 36 1843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061855
X-RAY DIFFRACTIONf_angle_d0.9332533
X-RAY DIFFRACTIONf_dihedral_angle_d15.5811051
X-RAY DIFFRACTIONf_chiral_restr0.048298
X-RAY DIFFRACTIONf_plane_restr0.01304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.43491490.39842660X-RAY DIFFRACTION100
1.8819-1.98110.34681440.34742637X-RAY DIFFRACTION100
1.9811-2.10510.29741430.29232620X-RAY DIFFRACTION100
2.1051-2.26740.24721410.26232640X-RAY DIFFRACTION100
2.2674-2.49520.25081340.24992674X-RAY DIFFRACTION100
2.4952-2.85540.22731300.21992645X-RAY DIFFRACTION100
2.8554-3.59440.20881420.20242665X-RAY DIFFRACTION100
3.5944-20.44270.24911540.23942682X-RAY DIFFRACTION100

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