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- PDB-9f9d: Laser excitation effects on BR: Dark dataset recorded at SwissFEL -

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Basic information

Entry
Database: PDB / ID: 9f9d
TitleLaser excitation effects on BR: Dark dataset recorded at SwissFEL
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Bacteriorhodospin / Membrane / RETINAL / TIME-RESOLVED CRYSTALLOGRAPHY / SERIAL CRYSTALLOGRAPHY / Laser excitation
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
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: 1.7 Å
AuthorsBertrand, Q. / Weinert, T. / Standfuss, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Innosuisse42711.1 IP-LSEuropean Union
CitationJournal: Nat Commun / Year: 2024
Title: Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate.
Authors: Bertrand, Q. / Nogly, P. / Nango, E. / Kekilli, D. / Khusainov, G. / Furrer, A. / James, D. / Dworkowski, F. / Skopintsev, P. / Mous, S. / Martiel, I. / Borjesson, P. / Ortolani, G. / Huang, ...Authors: Bertrand, Q. / Nogly, P. / Nango, E. / Kekilli, D. / Khusainov, G. / Furrer, A. / James, D. / Dworkowski, F. / Skopintsev, P. / Mous, S. / Martiel, I. / Borjesson, P. / Ortolani, G. / Huang, C.Y. / Kepa, M. / Ozerov, D. / Brunle, S. / Panneels, V. / Tanaka, T. / Tanaka, R. / Tono, K. / Owada, S. / Johnson, P.J.M. / Nass, K. / Knopp, G. / Cirelli, C. / Milne, C. / Schertler, G. / Iwata, S. / Neutze, R. / Weinert, T. / Standfuss, J.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)34,99919
Polymers25,2621
Non-polymers9,73718
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-52 kcal/mol
Surface area12820 Å2
Unit cell
Length a, b, c (Å)62.950, 62.950, 111.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

21A-449-

HOH

31A-450-

HOH

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 25261.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945
#2: 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.: 12 / Source method: obtained synthetically / Formula: C42H86O3
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-RET / RETINAL / BR / Bacterioopsin / BO


Mass: 284.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / 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: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.02989 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02989 Å / Relative weight: 1
ReflectionResolution: 1.65→16.02 Å / Num. obs: 30124 / % possible obs: 100 % / Redundancy: 186 % / CC star: 0.996 / R split: 0.0966 / Net I/σ(I): 9.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 123 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2996 / CC star: 0.833 / R split: 0.7139 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→16.02 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1718 2004 7.29 %
Rwork0.1381 --
obs0.1405 27497 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→16.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 254 51 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192158
X-RAY DIFFRACTIONf_angle_d1.5242872
X-RAY DIFFRACTIONf_dihedral_angle_d15.374456
X-RAY DIFFRACTIONf_chiral_restr0.114314
X-RAY DIFFRACTIONf_plane_restr0.016340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.26061410.24831781X-RAY DIFFRACTION100
1.74-1.790.28031400.21061838X-RAY DIFFRACTION100
1.79-1.840.26611440.1911816X-RAY DIFFRACTION100
1.84-1.90.22391420.18551801X-RAY DIFFRACTION100
1.9-1.970.18391430.13841827X-RAY DIFFRACTION100
1.97-2.050.17681420.1311796X-RAY DIFFRACTION100
2.05-2.140.15161470.10841819X-RAY DIFFRACTION100
2.14-2.250.14431480.11591837X-RAY DIFFRACTION100
2.25-2.390.1691370.1081798X-RAY DIFFRACTION100
2.39-2.580.15251410.1211840X-RAY DIFFRACTION100
2.58-2.840.14611420.12681831X-RAY DIFFRACTION100
2.84-3.240.15351430.1431822X-RAY DIFFRACTION100
3.25-4.070.16291490.13271829X-RAY DIFFRACTION100
4.08-16.020.18511450.1471858X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90550.3585-1.52854.7688-3.14089.0261-0.08750.136-0.1733-0.2297-0.0649-0.39810.39280.46910.19790.18750.0253-0.00540.2204-0.01860.303823.750827.294130.395
21.7502-0.2387-0.43432.16421.0464.3828-0.0495-0.2726-0.10060.37480.0535-0.04750.525-0.1241-0.00740.26680.0062-0.02870.22610.03540.269615.286528.068141.0101
34.9739-0.97520.43092.141-1.42554.06740.07780.54830.1997-0.8759-0.09530.1143-0.3896-0.48220.02760.52210.03140.00770.45630.01720.285713.09440.001914.8358
42.2587-0.04190.1472.22711.06375.3068-0.0355-0.1836-0.03980.21220.04780.03090.0324-0.1916-0.02720.20860.0229-0.02920.20880.0150.219612.065439.296840.6839
52.04790.1975-1.53222.1679-0.34932.26390.1625-0.04260.078-0.04330.17890.02350.1652-0.0624-0.33090.18790.0141-0.02970.16390.0020.22597.175246.664434.1745
63.0918-0.02860.32092.8246-1.56277.43590.0539-0.04830.23090.2524-0.0478-0.1702-0.58320.27850.01410.2219-0.0215-0.01380.1881-0.01460.268713.206453.621532.7616
71.8138-0.24611.00561.4916-1.23265.10060.0016-0.4910.0520.59150.027-0.2338-0.67060.1265-0.07880.3593-0.0221-0.07980.2933-0.02390.238521.378345.789545.9182
81.5373-0.3250.08771.1437-0.48763.77340.00050.08990.09790.00060.0492-0.1984-0.25690.1469-0.02630.1958-0.0271-0.02460.23440.00240.288923.501839.79229.7715
95.4858-2.0798-5.38234.48052.71885.7488-0.4474-0.5747-0.21111.09120.1153-0.93830.60050.88550.41670.52090.0396-0.16010.55710.11630.428824.491431.900954.4407
104.0153-1.93763.57010.9648-1.86433.84090.98-0.3561-0.57771.1096-0.08320.06360.80410.5807-0.92520.992-0.0831-0.12010.55820.05850.36919.238230.332164.8258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 154 )
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 191 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 224 )
9X-RAY DIFFRACTION9chain 'A' and (resid 225 through 229 )
10X-RAY DIFFRACTION10chain 'A' and (resid 230 through 234 )

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