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- PDB-6rqp: Steady-state-SMX dark state structure of bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 6rqp
TitleSteady-state-SMX dark state structure of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / retinal / serial crystallography / time-resolved / TR-SMX
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
Chem-LI1 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWeinert, T. / Skopintsev, P. / James, D. / Kekilli, D. / Furrer, A. / Bruenle, S. / Mous, S. / Nogly, P. / Standfuss, J.
CitationJournal: Science / Year: 2019
Title: Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography.
Authors: Weinert, T. / Skopintsev, P. / James, D. / Dworkowski, F. / Panepucci, E. / Kekilli, D. / Furrer, A. / Brunle, S. / Mous, S. / Ozerov, D. / Nogly, P. / Wang, M. / Standfuss, J.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,9729
Polymers25,0621
Non-polymers3,9118
Water41423
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,91727
Polymers75,1853
Non-polymers11,73224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12720 Å2
ΔGint-124 kcal/mol
Surface area27000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 62.000, 110.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 25061.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 4 / Source method: obtained synthetically / Formula: C42H86O3
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
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: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.8 Å / Num. obs: 22272 / % possible obs: 100 % / Redundancy: 1587.9 % / Biso Wilson estimate: 49.43 Å2 / CC1/2: 0.99 / R split: 0.026 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 198.2 % / Mean I/σ(I) obs: 1.17 / CC1/2: 0.31 / R split: 1.06 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Jet diameter: 50 µm

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.7data reduction
CrystFEL0.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G7H

6g7h


Resolution: 1.8→30.336 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.07
RfactorNum. reflection% reflection
Rfree0.1984 1346 6.04 %
Rwork0.1739 --
obs0.1753 22272 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.55 Å2 / Biso mean: 73.7603 Å2 / Biso min: 45.71 Å2
Refinement stepCycle: final / Resolution: 1.8→30.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 288 23 2081
Biso mean--97.39 71.76 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.86440.46441380.45620922230
1.8644-1.9390.44081360.371920872223
1.939-2.02720.34981300.318220942224
2.0272-2.13410.26831300.258620882218
2.1341-2.26770.22871380.202620662204
2.2677-2.44280.20911400.145720862226
2.4428-2.68850.17361300.125221052235
2.6885-3.07720.17351320.129920972229
3.0772-3.87560.15631340.154320942228
3.8756-30.34050.1991380.177621172255

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