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- PDB-6g7h: Retinal isomerization in bacteriorhodopsin revealed by a femtosec... -

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Basic information

Entry
Database: PDB / ID: 6g7h
TitleRetinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / retinal isomerization / ultrafast / femtosecond / room temperature / time resolved crystallography
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / 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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNogly, P. / Weinert, T. / James, D. / Cabajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. ...Nogly, P. / Weinert, T. / James, D. / Cabajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. / Lane, T. / Kekilli, D. / Bruenle, S. / Tanaka, T. / Wu, W. / Milne, C. / White, T. / Barty, A. / Weierstall, U. / Panneels, V. / Nango, E. / Iwata, S. / Hunter, M. / Schapiro, I. / Schertler, G. / Neutze, R. / Standfuss, J.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_159558 Switzerland
Swiss National Science Foundation310030_153145 Switzerland
Swiss National Science FoundationPZ00P3_174169 Switzerland
European Commission290605 Switzerland
CitationJournal: Science / Year: 2018
Title: Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.
Authors: Nogly, P. / Weinert, T. / James, D. / Carbajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. ...Authors: Nogly, P. / Weinert, T. / James, D. / Carbajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. / Lane, T. / Kekilli, D. / Brunle, S. / Tanaka, T. / Wu, W. / Milne, C. / White, T. / Barty, A. / Weierstall, U. / Panneels, V. / Nango, E. / Iwata, S. / Hunter, M. / Schapiro, I. / Schertler, G. / Neutze, R. / Standfuss, J.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Jan 17, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,99913
Polymers26,8141
Non-polymers6,18512
Water1,02757
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,99739
Polymers80,4433
Non-polymers18,55436
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
Unit cell
Length a, b, c (Å)62.320, 62.320, 111.100
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: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / 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
#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.: 7 / Source method: obtained synthetically / Formula: C42H86O3
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.04 % / Description: plates
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

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.5→19.355 Å / Num. obs: 39064 / % possible obs: 100 % / Redundancy: 2005.6 % / CC1/2: 0.999 / R split: 0.027 / Net I/σ(I): 19
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 122.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3893 / CC1/2: 0.084 / R split: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J7A

5j7a


Resolution: 1.5→19.355 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.96
RfactorNum. reflection% reflection
Rfree0.1428 2363 6.06 %
Rwork0.1151 --
obs0.1167 38966 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 193 57 2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172019
X-RAY DIFFRACTIONf_angle_d1.4032706
X-RAY DIFFRACTIONf_dihedral_angle_d14.2311162
X-RAY DIFFRACTIONf_chiral_restr0.26306
X-RAY DIFFRACTIONf_plane_restr0.012315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53060.22071620.17912098X-RAY DIFFRACTION99
1.5306-1.56390.21641130.15012185X-RAY DIFFRACTION100
1.5639-1.60020.16591230.12132137X-RAY DIFFRACTION100
1.6002-1.64020.14861430.09382160X-RAY DIFFRACTION100
1.6402-1.68460.14991390.08622162X-RAY DIFFRACTION100
1.6846-1.73410.14161370.07732115X-RAY DIFFRACTION100
1.7341-1.790.13431380.07522158X-RAY DIFFRACTION100
1.79-1.8540.12641400.07112137X-RAY DIFFRACTION100
1.854-1.92810.11291430.06512155X-RAY DIFFRACTION100
1.9281-2.01580.11971540.0662138X-RAY DIFFRACTION100
2.0158-2.1220.1041220.06252170X-RAY DIFFRACTION100
2.122-2.25470.10621510.06812137X-RAY DIFFRACTION100
2.2547-2.42850.11751420.07212155X-RAY DIFFRACTION100
2.4285-2.67230.12761390.08592155X-RAY DIFFRACTION100
2.6723-3.05770.12651300.09832177X-RAY DIFFRACTION100
3.0577-3.84740.12531450.12912177X-RAY DIFFRACTION100
3.8474-19.35630.18481420.16262187X-RAY DIFFRACTION100

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