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- PDB-6rnj: TR-SMX closed state structure (0-5ms) of bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 6rnj
TitleTR-SMX closed state structure (0-5ms) of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Retinal / time-resolved crystallography / serial crystallography / SMX
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsWeinert, T. / Skopintsev, P. / James, D. / Kekilli, D. / Furrer, F. / Bruenle, S. / Mous, S. / Nogly, P. / Standfuss, J.
CitationJournal: Science / Year: 2019
Title: Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography.
Authors: Weinert, T. / Skopintsev, P. / James, D. / Dworkowski, F. / Panepucci, E. / Kekilli, D. / Furrer, A. / Brunle, S. / Mous, S. / Ozerov, D. / Nogly, P. / Wang, M. / Standfuss, J.
History
DepositionMay 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,3462
Polymers25,0621
Non-polymers2841
Water1448
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0386
Polymers75,1853
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6220 Å2
ΔGint-49 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 62.000, 110.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 25061.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 5.6 / Details: 100 mM Na/K Phosphate buffer pH 5.6 30 % PEG 2000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981Y
22981Y
32981Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21
SYNCHROTRONSLS X06SA31
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJul 22, 2018
DECTRIS EIGER X 16M2PIXELJul 22, 2018
DECTRIS EIGER X 16M3PIXELJul 22, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SiSINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
31
Reflection

Entry-ID: 6RNJ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Diffraction-IDNet I/σ(I)CC1/2R split
2.6-38.47673790.1162.0411
2.3-38.510589100257.426.950.990.074
2.1-38.513882100984.9313.30.990.034
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible allNum. unique obsCC1/2R split
2.6-2.9811184
2.3-2.3770.50.922100133460.061.53
2.1-2.1824.61.333100138820.520.86
Serial crystallography sample delivery
IDMethod
1injection
2injection
3injection
Serial crystallography sample delivery injection
IDCarrier solventCrystal conc.DescriptionInjector nozzleInjector temperature (K)Jet diameter (µm)
1LCP13high viscosity injectorglass capillary29850
2LCP13flass capillary50

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.7data reduction
CrystFEL0.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6Z

5b6z


Resolution: 2.6→38.47 Å / SU ML: 0.5373 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 44.8015
RfactorNum. reflection% reflection
Rfree0.3012 419 6.22 %
Rwork0.2494 --
obs0.2529 6737 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 8 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271838
X-RAY DIFFRACTIONf_angle_d0.4472510
X-RAY DIFFRACTIONf_chiral_restr0.0347294
X-RAY DIFFRACTIONf_plane_restr0.003306
X-RAY DIFFRACTIONf_dihedral_angle_d9.85721046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.4751270.37191926X-RAY DIFFRACTION83.76
2.98-3.750.3571510.29032092X-RAY DIFFRACTION91.22
3.75-38.480.25391410.21492300X-RAY DIFFRACTION97.33

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