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- PDB-7vso: Serial Femtosecond Crystallography (SFX) of Ground State Bacterio... -

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Basic information

Entry
Database: PDB / ID: 7vso
TitleSerial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with HAD16 Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump / transport protein / retinal / proton transport
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
Similarity search - Domain/homology
Chem-7YH / DECANE / DODECANE / nonane / HEPTANE / IODIDE ION / N-OCTANE / HEXADECANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMizohata, E. / Nakane, T. / Hanashima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17GB Japan
CitationJournal: Membranes (Basel) / Year: 2021
Title: Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins.
Authors: Hanashima, S. / Nakane, T. / Mizohata, E.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)31,06621
Polymers26,9301
Non-polymers4,13620
Water57632
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13242
Polymers53,8592
Non-polymers8,27340
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6140 Å2
ΔGint-64 kcal/mol
Surface area18850 Å2
MethodPISA
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-431-

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

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Non-polymers , 11 types, 52 molecules

#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: Chemical ChemComp-7YH / 2-[[(2R)-2-(3-bromanyl-5-iodanyl-phenyl)carbonyloxy-3-tetradecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium


Mass: 777.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H49BrINO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#6: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H16 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 REMARK 280 NAH2PO4, 3.5%(W/V) TRIETHYLENE GLYCOL, 180 MM 1,6-HEXANEDIOL, 4 MM HAD16

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.771 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.35→42.9 Å / Num. obs: 13211 / % possible obs: 100 % / Redundancy: 206.2 % / CC1/2: 0.991 / Net I/σ(I): 7.34
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 897 / CC1/2: 0.488

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
CrystFELdata reduction
CrystFELdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B35

5b35


Resolution: 2.35→42.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.393 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20982 650 4.9 %RANDOM
Rwork0.15761 ---
obs0.16025 12530 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 79.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---1.21 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.35→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 253 32 2026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9552.0882759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6455223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4422.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50115283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.637157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211356
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.1697.272895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.99210.9211117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.3098.3531175
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.68271.5468196
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.323 41 -
Rwork0.329 897 -
obs--100 %

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