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- PDB-9f9h: Laser excitation effects on BR: Reprocessed Extrapolated 10ps Lig... -

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Basic information

Entry
Database: PDB / ID: 9f9h
TitleLaser excitation effects on BR: Reprocessed Extrapolated 10ps Light dataset recorded at 525 GW/cm2 from Nogly et al.
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: 1.66 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)34,64218
Polymers25,2621
Non-polymers9,38017
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-53 kcal/mol
Surface area12450 Å2
MethodPISA
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

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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.: 4 / 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.: 40 / 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 / 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: N
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: 1.55→19.35 Å / Num. obs: 35453 / % possible obs: 100 % / Redundancy: 194 % / CC star: 0.992 / R split: 0.083 / Net I/σ(I): 9.19
Reflection shellResolution: 1.55→1.6 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 3534 / CC star: 0.729 / R split: 0.9952 / % 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: 1.66→16.02 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 1983 7.15 %
Rwork0.2308 --
obs0.2335 27736 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→16.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 235 40 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192122
X-RAY DIFFRACTIONf_angle_d1.5862824
X-RAY DIFFRACTIONf_dihedral_angle_d16.576810
X-RAY DIFFRACTIONf_chiral_restr0.1311
X-RAY DIFFRACTIONf_plane_restr0.019332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.58491150.54321510X-RAY DIFFRACTION76
1.7-1.750.47031280.47811684X-RAY DIFFRACTION87
1.75-1.80.42551390.39421770X-RAY DIFFRACTION90
1.8-1.860.38511320.38121804X-RAY DIFFRACTION91
1.86-1.920.34081420.31641820X-RAY DIFFRACTION94
1.92-20.32221470.27511859X-RAY DIFFRACTION95
2-2.090.27571460.23041881X-RAY DIFFRACTION96
2.09-2.20.26051460.2141878X-RAY DIFFRACTION97
2.2-2.340.25581460.19791907X-RAY DIFFRACTION97
2.34-2.520.26621520.19911888X-RAY DIFFRACTION96
2.52-2.770.21861430.19511913X-RAY DIFFRACTION98
2.77-3.170.2441490.19091920X-RAY DIFFRACTION98
3.17-3.980.23491450.20031940X-RAY DIFFRACTION98
3.98-16.020.22681530.20271979X-RAY DIFFRACTION99
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)
11.63571.1773-1.67814.137-4.49787.8664-0.19150.0874-0.1939-0.2566-0.0761-0.4250.63530.62990.12880.13040.04140.01560.1592-0.01580.320723.666327.369429.9601
21.03880.1062-0.75211.65531.70132.3422-0.0302-0.1035-0.08180.2446-0.0008-0.06720.2661-0.0720.06050.12990.0081-0.01780.10510.01570.253415.31827.9941.4823
31.2786-0.3343-0.31891.41861.13795.83380.04060.18440.0772-0.11590.01-0.1161-0.10280.0484-0.06120.0974-0.00590.00280.12970.01870.237312.765738.99528.7212
41.6807-0.2885-0.20781.3661-0.74137.21130.1293-0.20220.00640.07450.17360.03690.1001-0.2567-0.28750.12350.0198-0.01390.1484-0.00160.2467.584946.331337.5348
51.7862-0.54950.68941.5846-2.06993.80330.0450.02760.13740.18420.0447-0.0454-0.5650.33410.03880.1282-0.0326-0.02410.1157-0.01050.2613.104553.584132.9633
65.3697-5.29264.96725.9973-6.01996.2149-0.5055-0.91650.50791.27140.80680.0613-1.2948-1.0154-0.3210.7186-0.0299-0.01110.74290.07180.508617.693646.883858.0517
70.6301-0.0964-0.64970.8498-0.77024.066-0.03070.0454-0.04870.09780.0096-0.1688-0.32250.28020.02810.1112-0.0487-0.03770.16910.01670.25422.968642.318935.4743
85.0444-0.75452.25661.49-2.46884.3081-0.0797-0.077-0.08810.49030.0193-0.45820.64570.6893-0.00070.33960.0043-0.17750.52390.09360.190423.769432.048156.4697
95.3156-3.23093.30361.9584-2.00352.05060.4446-0.8309-0.46420.4602-0.1308-0.0530.3901-0.2604-0.3450.6973-0.0751-0.11820.35780.05610.165919.167830.332965.0597
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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