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- PDB-5j7a: Bacteriorhodopsin ground state structure obtained with Serial Fem... -

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Basic information

Entry
Database: PDB / ID: 5j7a
TitleBacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / light-driven proton pump / retinal binding / seven transmembrane helix protein
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 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNogly, P. / Panneels, V. / Nelson, G. / Gati, C. / Kimura, T. / Milne, C. / Milathianaki, D. / Kubo, M. / Wu, W. / Conrad, C. ...Nogly, P. / Panneels, V. / Nelson, G. / Gati, C. / Kimura, T. / Milne, C. / Milathianaki, D. / Kubo, M. / Wu, W. / Conrad, C. / Coe, J. / Bean, R. / Zhao, Y. / Bath, P. / Dods, R. / Harimoorthy, R. / Beyerlein, K.R. / Rheinberger, J. / James, D. / DePonte, D. / Li, C. / Sala, L. / Williams, G. / Hunter, M. / Koglin, J.E. / Berntsen, P. / Nango, E. / Iwata, S. / Chapman, H.N. / Fromme, P. / Frank, M. / Abela, R. / Boutet, S. / Barty, A. / White, T.A. / Weierstall, U. / Spence, J. / Neutze, R. / Schertler, G. / Standfuss, J.
Citation
Journal: Nat Commun / Year: 2016
Title: Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.
Authors: Nogly, P. / Panneels, V. / Nelson, G. / Gati, C. / Kimura, T. / Milne, C. / Milathianaki, D. / Kubo, M. / Wu, W. / Conrad, C. / Coe, J. / Bean, R. / Zhao, Y. / Bath, P. / Dods, R. / ...Authors: Nogly, P. / Panneels, V. / Nelson, G. / Gati, C. / Kimura, T. / Milne, C. / Milathianaki, D. / Kubo, M. / Wu, W. / Conrad, C. / Coe, J. / Bean, R. / Zhao, Y. / Bath, P. / Dods, R. / Harimoorthy, R. / Beyerlein, K.R. / Rheinberger, J. / James, D. / DePonte, D. / Li, C. / Sala, L. / Williams, G.J. / Hunter, M.S. / Koglin, J.E. / Berntsen, P. / Nango, E. / Iwata, S. / Chapman, H.N. / Fromme, P. / Frank, M. / Abela, R. / Boutet, S. / Barty, A. / White, T.A. / Weierstall, U. / Spence, J. / Neutze, R. / Schertler, G. / Standfuss, J.
#1: Journal: IUCrJ / Year: 2015
Title: Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
Authors: Nogly, P. / James, D. / Wang, D. / White, T.A. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. / Jaeger, K. / Metz, M. / Wickstrand, C. / Wu, W. / Bath, P. ...Authors: Nogly, P. / James, D. / Wang, D. / White, T.A. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. / Jaeger, K. / Metz, M. / Wickstrand, C. / Wu, W. / Bath, P. / Berntsen, P. / Oberthuer, D. / Panneels, V. / Cherezov, V. / Chapman, H. / Schertler, G. / Neutze, R. / Spence, J. / Moraes, I. / Burghammer, M. / Standfuss, J. / Weierstall, U.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Jan 10, 2024Group: 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
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)28,3427
Polymers24,8611
Non-polymers3,4806
Water30617
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,02521
Polymers74,5843
Non-polymers10,44018
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 area13770 Å2
ΔGint-150 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 62.000, 110.000
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: 24861.422 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 / Tissue: PURPLE MEMBRANE / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#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.: 5 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 50.84 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: Precipitant: 29%-38% PEG 2000, 100 mM phosphate buffer pH 5.6. MAG 9.9 used for LCP formation. Crystallization setup in Hamilton syringe with tube of LCP surrounded by precipitant.

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Data collection

DiffractionMean temperature: 293 K
Ambient temp details: sample was injected into vacuum chamber thus experienced cooling
Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.83 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.83 Å / Relative weight: 1
ReflectionResolution: 2.3→21.9 Å / Num. obs: 11027 / % possible obs: 99.98 % / Redundancy: 163 % / Biso Wilson estimate: 31.3 Å2 / Net I/σ(I): 6.56
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 1.58 / % possible all: 99.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
CrystFEL0.6.1data reduction
CrystFEL0.6.1data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H68

1h68


Resolution: 2.3→21.66 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.346 / SU ML: 0.16 / SU R Cruickshank DPI: 0.3625 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 650 6.1 %RANDOM
Rwork0.191 ---
obs0.1926 10010 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.83 Å2 / Biso mean: 39.282 Å2 / Biso min: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.72 Å20 Å2
2--1.45 Å2-0 Å2
3----4.69 Å2
Refinement stepCycle: final / Resolution: 2.3→21.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 77 17 1809
Biso mean--47.23 43.13 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211855
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9962487
X-RAY DIFFRACTIONr_angle_other_deg0.892.9864231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4525222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6322.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.008156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022406
X-RAY DIFFRACTIONr_mcbond_it0.371.724894
X-RAY DIFFRACTIONr_mcbond_other0.371.723893
X-RAY DIFFRACTIONr_mcangle_it0.6942.5781114
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 46 -
Rwork0.275 709 -
all-755 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 16.819 Å / Origin y: 39.321 Å / Origin z: 34.934 Å
111213212223313233
T0.018 Å2-0.0018 Å2-0.0354 Å2-0.0229 Å2-0.0059 Å2--0.5363 Å2
L1.4776 °2-0.3488 °2-0.2806 °2-2.4409 °2-0.0007 °2--0.9092 °2
S-0.0253 Å °-0.103 Å °0.0395 Å °0.2012 Å °0.0122 Å °-0.1565 Å °-0.0217 Å °0.1353 Å °0.0131 Å °

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