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- PDB-9f9i: Laser excitation effects on BR: Dark dataset recorded at SACLA -

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Basic information

Entry
Database: PDB / ID: 9f9i
TitleLaser excitation effects on BR: Dark dataset recorded at SACLA
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: 1.6 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)34,98419
Polymers25,2481
Non-polymers9,73718
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-54 kcal/mol
Surface area12780 Å2
Unit cell
Length a, b, c (Å)62.450, 62.450, 111.170
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: 25247.781 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.: 45 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.227 Å
DetectorType: MPCCD / Detector: CCD / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.227 Å / Relative weight: 1
ReflectionResolution: 1.59→31.23 Å / Num. obs: 32843 / % possible obs: 100 % / Redundancy: 1944 % / CC star: 0.999 / R split: 0.0423 / Net I/σ(I): 15.9
Reflection shellResolution: 1.59→1.64 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 3272 / CC star: 0.614 / R split: 0.8581 / % 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: 1.6→31.23 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1785 1994 6.16 %
Rwork0.1501 --
obs0.1518 32349 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 262 45 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112147
X-RAY DIFFRACTIONf_angle_d1.1822853
X-RAY DIFFRACTIONf_dihedral_angle_d15.746455
X-RAY DIFFRACTIONf_chiral_restr0.075312
X-RAY DIFFRACTIONf_plane_restr0.009335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29491430.26982166X-RAY DIFFRACTION100
1.64-1.680.28381380.24692165X-RAY DIFFRACTION100
1.68-1.730.28441420.21752151X-RAY DIFFRACTION100
1.73-1.790.23351430.19462166X-RAY DIFFRACTION100
1.79-1.850.23451370.16942145X-RAY DIFFRACTION100
1.85-1.930.18691390.15532180X-RAY DIFFRACTION100
1.93-2.020.17411420.13912177X-RAY DIFFRACTION100
2.02-2.120.15311430.14352152X-RAY DIFFRACTION100
2.12-2.260.1571390.12842173X-RAY DIFFRACTION100
2.26-2.430.16751420.12692166X-RAY DIFFRACTION100
2.43-2.670.16551490.13792157X-RAY DIFFRACTION100
2.67-3.060.14331410.14822180X-RAY DIFFRACTION100
3.06-3.850.17511440.13622190X-RAY DIFFRACTION100
3.86-31.230.18241520.15312187X-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)
13.36491.6116-2.62527.6121-5.67775.5236-0.13060.216-0.1499-0.299-0.0159-0.43760.40680.2210.18250.13650.0317-0.00370.187-0.02650.300923.632427.163729.821
22.1506-0.1371-0.48831.94591.36481.642-0.0448-0.3433-0.13190.4420.0475-0.0390.4377-0.09790.02310.26030.0165-0.02810.19180.04220.247915.202327.72841.1771
31.7658-0.3199-0.43272.52350.81751.24570.03150.22690.0066-0.29370.0089-0.0338-0.0568-0.1485-0.04110.1870.0064-0.01260.19980.01150.210212.642138.679428.641
41.83490.0335-0.87511.9448-2.18449.40670.1292-0.14430.02030.07930.19040.04870.1003-0.2312-0.34910.18270.0189-0.030.17060.00030.22937.549245.937637.1993
53.32060.10920.2862.9818-2.11295.57280.09-0.0250.23350.2464-0.0845-0.1232-0.51310.39490.04630.2045-0.0218-0.00310.1755-0.00870.257913.113253.187932.8403
65.5475-4.54465.61983.7842-4.6335.7085-0.9621-2.03211.04971.2310.5732-0.2086-2.3035-0.31610.37931.06710.034-0.04820.9261-0.07080.684317.704646.520957.7572
71.0925-0.1151-0.36641.2176-0.63593.1333-0.015-0.11890.05810.18940.0404-0.2686-0.26690.1377-0.02920.193-0.0315-0.04410.2375-0.00730.287722.913341.989735.2981
82.00021.9389-4.79163.0935-0.122.4753-0.1115-0.0355-0.63870.972-0.3657-1.50420.94381.720.00050.45370.0195-0.18020.66440.15610.489123.711831.456455.2073
93.6886-1.3441.69240.6396-0.16362.13660.4566-0.5697-0.43770.4034-0.01540.00590.4772-0.1632-0.31050.8047-0.0769-0.13860.53890.06780.215219.073130.06264.7397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 224 )
8X-RAY DIFFRACTION8chain 'A' and (resid 225 through 229 )
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 234 )

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