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- PDB-5b35: Serial Femtosecond Crystallography (SFX) of Ground State Bacterio... -

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Basic information

Entry
Database: PDB / ID: 5b35
TitleSerial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Membrane protein / Proton pump / Transport Protein / Retinal
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / protein domain specific binding / 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-4QM / DECANE / DODECANE / nonane / HEPTANE / N-OCTANE / HEXADECANE / RETINAL / Bacteriorhodopsin / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMizohata, E. / Nakane, T. / Suzuki, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
X-ray Free-Electron Laser Priority Strategy Program (MEXT)SACLA-SFX Project Japan
Japanese Society of Technology ERATOMurata Lipid Active Structure Project Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent
Authors: Nakane, T. / Hanashima, S. / Suzuki, M. / Saiki, H. / Hayashi, T. / Kakinouchi, K. / Sugiyama, S. / Kawatake, S. / Matsuoka, S. / Matsumori, N. / Nango, E. / Kobayashi, J. / Shimamura, T. / ...Authors: Nakane, T. / Hanashima, S. / Suzuki, M. / Saiki, H. / Hayashi, T. / Kakinouchi, K. / Sugiyama, S. / Kawatake, S. / Matsuoka, S. / Matsumori, N. / Nango, E. / Kobayashi, J. / Shimamura, T. / Kimura, K. / Mori, C. / Kunishima, N. / Sugahara, M. / Takakyu, Y. / Inoue, S. / Masuda, T. / Hosaka, T. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Inoue, T. / Nureki, O. / Iwata, S. / Murata, M. / Mizohata, E.
History
DepositionFeb 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)29,83918
Polymers26,9301
Non-polymers2,90917
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint27 kcal/mol
Surface area11600 Å2
Unit cell
Length a, b, c (Å)46.200, 103.000, 128.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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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 natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: R1M1 / References: UniProt: P02945, UniProt: B0R5N9*PLUS

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Non-polymers , 9 types, 53 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-4QM / (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol


Mass: 378.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H42O3
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-R16 / HEXADECANE / Hexadecane


Mass: 226.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34
#8: Chemical ChemComp-HP6 / HEPTANE / Heptane


Mass: 100.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16
#9: Chemical ChemComp-DD9 / nonane / Nonane


Mass: 128.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 25%(w/v) DMPC/CHAPSO bicelles, 3.2 M NaH2PO4, 3.5%(w/v) triethylene glycol, 180 mM 1,6-hexanediol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.771 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 13212 / % possible obs: 100 % / Redundancy: 80.9 % / Net I/σ(I): 4.83
Reflection shellResolution: 2.35→2.42 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Cheetahdata extraction
CrystFELdata processing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 5B34

5b34


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.863 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21978 650 4.9 %RANDOM
Rwork0.16633 ---
obs0.16905 12535 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 205 36 1986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021987
X-RAY DIFFRACTIONr_bond_other_d0.0020.022177
X-RAY DIFFRACTIONr_angle_refined_deg1.9452.052654
X-RAY DIFFRACTIONr_angle_other_deg1.08735009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80622.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70315283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.393157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02424
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8325.905899
X-RAY DIFFRACTIONr_mcbond_other3.825.901898
X-RAY DIFFRACTIONr_mcangle_it5.0448.8841122
X-RAY DIFFRACTIONr_mcangle_other5.0468.8861123
X-RAY DIFFRACTIONr_scbond_it5.3426.9011088
X-RAY DIFFRACTIONr_scbond_other5.346.9051089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6439.971533
X-RAY DIFFRACTIONr_long_range_B_refined9.10258.1898099
X-RAY DIFFRACTIONr_long_range_B_other9.09758.198095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 41 -
Rwork0.337 897 -
obs--100 %

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