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- PDB-6rph: TR-SMX open state structure (10-15ms) of bacteriorhodopsin -

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Open data


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Basic information

Entry
Database: PDB / ID: 6rph
TitleTR-SMX open state structure (10-15ms) of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Retinal / time resolved crystallography / serial crystallography / 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 / Resolution: 2.6 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 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2019Group: Advisory / Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_validate_close_contact
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_2

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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)26,5382
Polymers26,2541
Non-polymers2841
Water1267
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6156
Polymers78,7623
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 area6460 Å2
ΔGint-51 kcal/mol
Surface area29280 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
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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


Mass: 26254.041 Da / Num. of mol.: 1 / 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
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
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 16M1PIXELJul 22, 2018
DECTRIS EIGER X 16M2PIXELJul 22, 2018
DECTRIS EIGER X 16M3PIXELJul 22, 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: 6RPH

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Diffraction-IDNet I/σ(I)CC1/2R split
2.6-31647787.3158.1611
2.3-38.510589100254.926.770.990.075
2.1-38.513882100984.9313.30.990.034
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible allMean I/σ(I) obsCC1/2R split
2.6-2.9811838180
2.3-2.3720.940.131.73
2.1-2.1824.631001.330.520.86
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
PHENIX1.13_2998refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.6→31 Å / SU ML: 0.5951 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 52.0519
RfactorNum. reflection% reflection
Rfree0.3599 410 6.33 %
Rwork0.3173 --
obs0.3202 6477 87.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 92.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 7 1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161795
X-RAY DIFFRACTIONf_angle_d0.36822452
X-RAY DIFFRACTIONf_chiral_restr0.0341288
X-RAY DIFFRACTIONf_plane_restr0.0033298
X-RAY DIFFRACTIONf_dihedral_angle_d8.47251023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.54451240.47181838X-RAY DIFFRACTION80.08
2.98-3.750.45361450.36072016X-RAY DIFFRACTION87.99
3.75-310.29641410.27392213X-RAY DIFFRACTION93.75
Refinement TLS params.Method: refined / Origin x: 17.3727838803 Å / Origin y: 39.5874483686 Å / Origin z: 36.1591924597 Å
111213212223313233
T0.289842447348 Å2-0.0211474326615 Å2-0.0800332586199 Å2-0.414010604095 Å2-0.0357636784923 Å2--0.563079957839 Å2
L0.37772496754 °2-0.874924624088 °2-0.647410256314 °2-2.36362872118 °20.196618946642 °2--1.10523823566 °2
S0.0622769468753 Å °-0.142586650849 Å °0.0897547541725 Å °0.0789991643264 Å °0.0787203022347 Å °-0.087373560563 Å °-0.033226123333 Å °0.171061627379 Å °-0.0888945165204 Å °
Refinement TLS groupSelection details: all

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