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- PDB-6rqo: Steady-state-SMX activated state structure of bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 6rqo
TitleSteady-state-SMX activated state structure of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / retinal / serial crystallography / time-resolved crystallography / 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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7572
Polymers24,4731
Non-polymers2841
Water1448
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2726
Polymers73,4193
Non-polymers8533
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 area6210 Å2
ΔGint-48 kcal/mol
Surface area26890 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: 24472.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981Y
22981Y
32981Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21
SYNCHROTRONSLS X06SA31
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJun 5, 2018
DECTRIS EIGER X 16M2PIXELJun 5, 2018
DECTRIS EIGER X 16M3PIXELMay 6, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
31
Reflection

Entry-ID: 6RQO

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Diffraction-IDNet I/σ(I)CC1/2R split
2-30.41590398.1111
1.8-30.8219761001390.3212.40.990.024
1.8-30.8219771001587.9314.30.990.026
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible allMean I/σ(I) obsCC1/2R split
2-2.112127199
1.8-1.8558.1299.50.360.054
1.8-1.85198.231000.690.311.06
Serial crystallography sample delivery
IDMethod
1injection
2injection
3injection
Serial crystallography sample delivery injection
IDCarrier solventJet diameter (µm)
1LCP50
2LCP50
3LCP50

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.7data reduction
CrystFEL0.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6Z

5b6z


Resolution: 2→30.336 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 31.44
RfactorNum. reflection% reflection
Rfree0.2458 1011 6.36 %
Rwork0.2047 --
obs0.2074 15903 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.41 Å2 / Biso mean: 43.9909 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 2→30.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 40 16 1772
Biso mean--32.78 56.61 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.10560.35221330.31072127226099
2.1056-2.23750.27921620.23212092225498
2.2375-2.41020.28121450.19982142228799
2.4102-2.65260.24371340.17642104223897
2.6526-3.03620.2171460.16822111225797
3.0362-3.8240.24931560.19712139229598
3.824-30.33960.23381350.21012177231298
Refinement TLS params.Method: refined / Origin x: 17.0842 Å / Origin y: 39.525 Å / Origin z: 35.8918 Å
111213212223313233
T0.2483 Å2-0.0134 Å2-0.0616 Å2-0.3245 Å2-0.0112 Å2--0.331 Å2
L1.7175 °2-0.1987 °2-0.3052 °2-2.2982 °20.4412 °2--0.9962 °2
S-0.0283 Å °0.0147 Å °0.123 Å °-0.0314 Å °0.0143 Å °-0.2191 Å °-0.0187 Å °0.2449 Å °0.0384 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 501
2X-RAY DIFFRACTION1allB6 - 456

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