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- PDB-6ga6: Bacteriorhodopsin, 10 ps state, real-space refined against 10% ex... -

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Basic information

Entry
Database: PDB / ID: 6ga6
TitleBacteriorhodopsin, 10 ps state, real-space refined against 10% extrapolated map
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump / time-resolved crystallography / free-electron laser
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / 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 / Resolution: 1.8 Å
AuthorsNass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. ...Nass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Domratcheva, T. / Schlichting, I.
Funding support1items
OrganizationGrant numberCountry
ANR-17-CE11-0018-01
CitationJournal: Nat Commun / Year: 2019
Title: Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.
Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / ...Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J.E. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Heyne, K. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)30,79516
Polymers26,9301
Non-polymers3,86515
Water77543
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,38448
Polymers80,7893
Non-polymers11,59545
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 area24910 Å2
ΔGint-112 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.700, 61.700, 109.400
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: 26929.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945

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Non-polymers , 11 types, 58 molecules

#2: Chemical ChemComp-RET / RETINAL / 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 / Tridecane


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


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


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


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


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#9: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane


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


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


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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: 32% (w/v) PEG 2000, 0.1 M K2HPO4 /NaH2PO4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.26 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 21876 / % possible obs: 100 % / Redundancy: 187 % / R split: 0.119 / Net I/σ(I): 6.4
Reflection shellResolution: 1.8→1.9 Å / R split: 0.607

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementResolution: 1.8→20 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 0.33 / Phase error: 21
Details: A MOLECULE IS THE DARK STATE B MOLECULE WAS REAL-SPACE REFINED AGAINST MAP CALCULATED FROM EXTRAPOLATED STRUCTURE FACTORS (AT 10% OCCUPANCY) MODEL/MAP FIT (CCmask)=0.7785
RfactorNum. reflection% reflection
Rfree0.2162 1108 5.07 %
Rwork0.1981 --
obs0.199 21859 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 227 43 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073905
X-RAY DIFFRACTIONf_angle_d1.0145262
X-RAY DIFFRACTIONf_dihedral_angle_d16.1962211
X-RAY DIFFRACTIONf_chiral_restr0.046607
X-RAY DIFFRACTIONf_plane_restr0.012606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8820.25281390.27512579X-RAY DIFFRACTION100
1.882-1.98110.22761450.22522586X-RAY DIFFRACTION100
1.9811-2.10510.21841400.19622575X-RAY DIFFRACTION100
2.1051-2.26750.20941390.18812581X-RAY DIFFRACTION100
2.2675-2.49530.18031270.18852602X-RAY DIFFRACTION100
2.4953-2.85550.17711290.18112606X-RAY DIFFRACTION100
2.8555-3.59450.22131380.18412604X-RAY DIFFRACTION100
3.5945-20.46670.23681510.20852618X-RAY DIFFRACTION100

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