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- PDB-5b6v: A three dimensional movie of structural changes in bacteriorhodop... -

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Basic information

Entry
Database: PDB / ID: 5b6v
TitleA three dimensional movie of structural changes in bacteriorhodopsin: resting state structure
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / bacteriorhodopsin / XFEL / time-resolved SFX / SACLA
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
TETRADECANE / DECANE / nonane / HEPTANE / 2,3-DI-PHYTANYL-GLYCEROL / PENTADECANE / N-OCTANE / RETINAL / TRIDECANE / UNDECANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNango, E. / Royant, A. / Nakane, T. / Tanaka, T. / Arima, T. / Neutze, R. / Iwata, S.
CitationJournal: Science / Year: 2016
Title: A three-dimensional movie of structural changes in bacteriorhodopsin
Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / ...Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / Mizohata, E. / Nogly, P. / Sugahara, M. / Nam, D. / Nomura, T. / Shimamura, T. / Im, D. / Fujiwara, T. / Yamanaka, Y. / Jeon, B. / Nishizawa, T. / Oda, K. / Fukuda, M. / Andersson, R. / Bath, P. / Dods, R. / Davidsson, J. / Matsuoka, S. / Kawatake, S. / Murata, M. / Nureki, O. / Owada, S. / Kameshima, T. / Hatsui, T. / Joti, Y. / Schertler, G. / Yabashi, M. / Bondar, A.N. / Standfuss, J. / Neutze, R. / Iwata, S.
History
DepositionJun 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,89217
Polymers26,8141
Non-polymers4,07816
Water30617
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,67651
Polymers80,4433
Non-polymers12,23348
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area25220 Å2
ΔGint-117 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 62.500, 112.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP residues 14-261 / Source method: isolated from a natural source
Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945

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Non-polymers , 11 types, 33 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H88O3
#4: Chemical ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#7: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#8: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#9: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24
#10: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#11: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsLigands TRD, D10, HP6, OCT, MYS, UND, DD9, and C14 are modeled as a lipid fragment.

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.1M Na/K phosphate pH5.4 , 30% PEG 2000

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Data collection

DiffractionMean temperature: 293 K
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→39.92 Å / Num. obs: 16786 / % possible obs: 100 % / Redundancy: 3389 % / Net I/σ(I): 30
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NS0

3ns0


Resolution: 2→21.912 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1747 839 5.01 %
Rwork0.1502 --
obs0.1516 16745 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→21.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 242 17 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032063
X-RAY DIFFRACTIONf_angle_d0.7322744
X-RAY DIFFRACTIONf_dihedral_angle_d17.4721189
X-RAY DIFFRACTIONf_chiral_restr0.038310
X-RAY DIFFRACTIONf_plane_restr0.003299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12520.26611430.20712629X-RAY DIFFRACTION100
2.1252-2.28910.22181370.15032642X-RAY DIFFRACTION100
2.2891-2.51920.14741340.12852653X-RAY DIFFRACTION100
2.5192-2.8830.15771320.13242643X-RAY DIFFRACTION100
2.883-3.62960.16341400.14852671X-RAY DIFFRACTION100
3.6296-21.9130.17931530.15662668X-RAY DIFFRACTION100

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