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- PDB-9f9b: Laser excitation effects on BR: reprocessed dark dataset recorded... -

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Basic information

Entry
Database: PDB / ID: 9f9b
TitleLaser excitation effects on BR: reprocessed dark dataset recorded from Nango 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: 2 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)35,28119
Polymers25,2621
Non-polymers10,01918
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-59 kcal/mol
Surface area12590 Å2
Unit cell
Length a, b, c (Å)62.580, 62.580, 111.810
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-438-

HOH

21A-439-

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.: 13 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / Details: 100 mM Na/K Phosphate buffer pH 5.4 30 % PEG 2000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.63 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.63 Å / Relative weight: 1
ReflectionResolution: 2→38.9 Å / Num. obs: 17068 / % possible obs: 100 % / Redundancy: 783 % / CC star: 0.998 / R split: 0.0975 / Net I/σ(I): 9.75
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 1705 / CC star: 0.848 / R split: 0.7615
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.20_4487)refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.92 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 1663 9.93 %
Rwork0.1435 --
obs0.1475 16753 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→21.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 245 40 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.075
X-RAY DIFFRACTIONf_dihedral_angle_d13.733442
X-RAY DIFFRACTIONf_chiral_restr0.07313
X-RAY DIFFRACTIONf_plane_restr0.007335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.32971400.28261217X-RAY DIFFRACTION100
2.06-2.130.24511400.20021279X-RAY DIFFRACTION100
2.13-2.20.19791380.1581235X-RAY DIFFRACTION100
2.2-2.290.20591370.15911263X-RAY DIFFRACTION100
2.29-2.390.17551350.12611260X-RAY DIFFRACTION100
2.39-2.520.18851420.1351266X-RAY DIFFRACTION100
2.52-2.680.19361380.12511241X-RAY DIFFRACTION100
2.68-2.880.19491320.13481250X-RAY DIFFRACTION100
2.88-3.170.18081400.13471284X-RAY DIFFRACTION100
3.17-3.630.1581410.13691247X-RAY DIFFRACTION100
3.63-4.570.16271320.12681271X-RAY DIFFRACTION100
4.57-21.920.18951480.15821277X-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)
10.65970.356-0.51861.2141-0.42640.4245-0.09080.1109-0.1951-0.13070.0649-0.27680.48410.1994-0.00040.33590.02750.00870.3347-0.01420.407123.664727.069830.0497
20.1416-0.135-0.10670.20770.20850.22720.0006-0.0275-0.07960.0920.1044-0.03610.4303-0.18-00.3890.0107-0.03290.31570.04440.356315.241127.799141.2478
30.5681-0.1297-0.13750.8270.4040.20670.00270.0610.0463-0.10520.02760.0735-0.0726-0.094-0.00010.28360.0151-0.02580.28630.01540.272710.753541.405532.8823
40.10160.0321-0.0610.4216-0.32580.26090.03560.12010.10340.059-0.0326-0.1891-0.42970.1523-0.00040.3567-0.02-0.01280.3593-0.0020.347612.352752.870230.3792
50.28030.1128-0.05750.139-0.00670.0146-0.4231-0.55240.4119-0.19530.48950.5574-0.3369-0.0146-0.0090.9209-0.1322-0.08970.70380.07840.419817.651747.928657.0085
60.10850.0013-0.2279-0.0004-0.00260.4566-0.00230.01930.0190.04990.0203-0.2809-0.22540.2406-00.3364-0.0339-0.04840.32850.01320.351722.869142.14835.5983
70.87760.0192-0.83951.85090.64161.0381-0.15650.2180.20020.7533-0.3695-0.10730.10970.2441-0.38720.6672-0.0104-0.09340.58810.08670.363322.178331.013158.8862
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 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 224 )
7X-RAY DIFFRACTION7chain 'A' and (resid 225 through 234 )

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