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- PDB-7q38: Crystal structure of the mutant bacteriorhodopsin pressurized wit... -

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Basic information

Entry
Database: PDB / ID: 7q38
TitleCrystal structure of the mutant bacteriorhodopsin pressurized with argon
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump rhodopsin
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / 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
ARGON / HEXANE / EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMelnikov, I. / Rulev, M. / Astashkin, R. / Kovalev, K. / Carpentier, P. / Gordeliy, V. / Popov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action.
Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / ...Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / Mueller-Dieckmann, C. / van der Linden, P. / Carpentier, P. / Leonard, G. / Gordeliy, V. / Popov, A.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)35,77469
Polymers29,0461
Non-polymers6,72868
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-1 kcal/mol
Surface area11960 Å2
Unit cell
Length a, b, c (Å)115.657, 119.245, 36.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-302-

LFA

21A-320-

SO4

31A-320-

SO4

41A-335-

AR

51A-362-

AR

61A-477-

HOH

71A-512-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 29045.801 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 / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945

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Non-polymers , 8 types, 187 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical...
ChemComp-AR / ARGON


Mass: 39.948 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Ar / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 3.0 M Ammonium Sulfate,0.1 M Sodium Acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97241 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 57738 / % possible obs: 99 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 16.29
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 4476 / CC1/2: 0.34 / Rrim(I) all: 1.769 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XXJ

4xxj


Resolution: 1.65→83.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.872 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20522 1569 5.1 %RANDOM
Rwork0.16232 ---
obs0.16452 29182 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.514 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2---0.67 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.65→83.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 296 119 2152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132119
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172284
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6512837
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5635283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0145262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40619.71871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.897155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02440
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_it2.0772.354952
X-RAY DIFFRACTIONr_mcbond_other2.0482.345950
X-RAY DIFFRACTIONr_mcangle_it3.0413.5241200
X-RAY DIFFRACTIONr_mcangle_other3.0463.5231200
X-RAY DIFFRACTIONr_scbond_it3.6393.1411166
X-RAY DIFFRACTIONr_scbond_other3.5113.1291159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0954.3611609
X-RAY DIFFRACTIONr_long_range_B_refined7.13263.9312495
X-RAY DIFFRACTIONr_long_range_B_other7.13435.9772492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 113 -
Rwork0.506 2097 -
obs--99.68 %

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