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- PDB-5zin: Crystal structure of bacteriorhodopsin at 1.27 A resolution -

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Basic information

Entry
Database: PDB / ID: 5zin
TitleCrystal structure of bacteriorhodopsin at 1.27 A resolution
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / proton pump / membrane 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
2,3-DI-PHYTANYL-GLYCEROL / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsHasegawa, N. / Jonotsuka, H. / Miki, K. / Takeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS25440020, 17H03643 Japan
CitationJournal: Sci Rep / Year: 2018
Title: X-ray structure analysis of bacteriorhodopsin at 1.3 angstrom resolution.
Authors: Hasegawa, N. / Jonotsuka, H. / Miki, K. / Takeda, K.
History
DepositionMar 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 2.0May 5, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _cell.angle_alpha_esd / _cell.angle_beta_esd / _cell.angle_gamma_esd / _cell.length_a_esd / _cell.length_b_esd / _cell.length_c_esd / _entity.formula_weight / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Nov 22, 2023Group: 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)27,2345
Polymers24,9911
Non-polymers2,2444
Water50428
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70315
Polymers74,9723
Non-polymers6,73212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
Buried area15260 Å2
ΔGint-137 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.630, 60.630, 110.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 24990.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (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
#3: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H88O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: MO, 2.0-2.5 M phosphate

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Data collection

DiffractionMean temperature: 15 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.478
ReflectionResolution: 1.27→47 Å / Num. obs: 60573 / % possible obs: 100 % / Redundancy: 81.457 % / Biso Wilson estimate: 23.589 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.134 / Χ2: 1.013 / Net I/σ(I): 22.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.27-1.377.3664.3311.0944890.514.359100
1.3-1.3479.8983.9131.343620.5433.938100
1.34-1.3879.0453.0131.8542270.6653.032100
1.38-1.4282.572.3522.5741170.772.366100
1.42-1.4783.7211.8343.4539940.831.845100
1.47-1.5283.2241.3954.7838890.9321.403100
1.52-1.5882.331.0996.3136710.9311.106100
1.58-1.6478.6280.8028.736310.9590.807100
1.64-1.7182.1640.63611.333890.9740.64100
1.71-1.881.3250.48115.2133080.9830.484100
1.8-1.8986.1140.36320.6931270.9920.365100
1.89-2.0185.1050.26128.7229860.9960.262100
2.01-2.1582.840.17240.0427570.9980.173100
2.15-2.3278.0150.14647.4826100.9990.147100
2.32-2.5480.210.11656.9323680.9990.117100
2.54-2.8482.6630.09668.121610.9990.097100
2.84-3.2884.0480.0878.519050.9990.081100
3.28-4.0278.2860.06787.09164110.067100
4.02-5.6878.9150.0693.36123910.06100
5.68-4786.3960.0597.3570210.0599.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXLrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.27→47 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1631 3028 -
Rwork0.1303 --
obs-60573 100 %
Displacement parametersBiso max: 79.95 Å2 / Biso mean: 28.289 Å2 / Biso min: 15.01 Å2
Refinement stepCycle: LAST / Resolution: 1.27→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 140 28 1930

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