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- PDB-4y9h: The 1.43 angstrom crystal structure of bacteriorhodopsin crystall... -

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Basic information

Entry
Database: PDB / ID: 4y9h
TitleThe 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles
ComponentsBacteriorhodopsin
KeywordsLIPID BINDING PROTEIN / bacteriorhodopsin / complex / membrane protein / Cell membrane / Multi-pass membrane protein
Function / homology
Function and homology information


photoreceptor activity / phototransduction / 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
DECANE / DODECANE / nonane / HEPTANE / PHOSPHATE ION / HEXADECANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSaiki, H. / Sugiyama, S. / Kakinouchi, K. / Kawatake, S. / Hanashima, S. / Matsumori, N. / Murata, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS KAKENHI25286051 Japan
JSPS KAKENHI25650051 Japan
CitationJournal: To Be Published
Title: The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles
Authors: Saiki, H. / Sugiyama, S. / Kakinouchi, K. / Kawatake, S. / Hanashima, S. / Matsumori, N. / Murata, M.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,52618
Polymers24,7601
Non-polymers2,76617
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint35 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)45.215, 102.794, 128.337
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-490-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin


Mass: 24760.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) (Halophile)
Strain: ATCC 29341 / DSM 671 / R1 / References: UniProt: B0R5N9

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Non-polymers , 8 types, 111 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#5: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#8: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 180mM 1,6-hexanediol, 2.6M NaH2PO4, 3.5% triethyleneglycol, pH4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 55216 / % possible obs: 99.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.675 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22102 2797 5.1 %RANDOM
Rwork0.19946 ---
obs0.20056 52375 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.844 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å2-0 Å2
2---0.98 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 193 94 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022051
X-RAY DIFFRACTIONr_bond_other_d0.0010.022257
X-RAY DIFFRACTIONr_angle_refined_deg2.2132.042752
X-RAY DIFFRACTIONr_angle_other_deg0.93935209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8775253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9882260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.529158
X-RAY DIFFRACTIONr_chiral_restr0.140.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212106
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
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_it2.1261.833933
X-RAY DIFFRACTIONr_mcbond_other2.1251.832933
X-RAY DIFFRACTIONr_mcangle_it3.0322.7441173
X-RAY DIFFRACTIONr_mcangle_other3.0352.7471174
X-RAY DIFFRACTIONr_scbond_it3.752.681118
X-RAY DIFFRACTIONr_scbond_other3.7492.6821119
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5273.631567
X-RAY DIFFRACTIONr_long_range_B_refined7.34116.4492364
X-RAY DIFFRACTIONr_long_range_B_other7.0216.0272329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.429→1.466 Å
Num. reflection% reflection
Rfree186 -
Rwork3528 -
obs-91.43 %

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