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- PDB-7q35: Crystal structure of the mutant bacteriorhodopsin pressurized wit... -

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Basic information

Entry
Database: PDB / ID: 7q35
TitleCrystal structure of the mutant bacteriorhodopsin pressurized with krypton
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / 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
Similarity search - Domain/homology
HEXANE / KRYPTON / EICOSANE / OLEIC ACID / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 23, 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)36,57355
Polymers29,0461
Non-polymers7,52754
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint33 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.330, 119.986, 36.461
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-319-

SO4

21A-319-

SO4

31A-334-

KR

41A-340-

KR

51A-341-

KR

61A-349-

KR

71A-499-

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 , 7 types, 160 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.: 11 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-OLA / OLEIC ACID


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


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical...
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
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: 0.8634 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8634 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 33739 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.149 / Net I/σ(I): 9.09
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 4700 / CC1/2: 0.517 / Rrim(I) all: 1.86 / % possible all: 99.8

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Processing

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

4xxj


Resolution: 2→41.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.063 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23199 838 4.8 %RANDOM
Rwork0.16949 ---
obs0.17238 16764 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---1.73 Å2-0 Å2
3---1.79 Å2
Refinement stepCycle: 1 / Resolution: 2→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 266 106 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131987
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172152
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6452636
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5464947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7265230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81418.95567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.316156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
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_it2.0032.619905
X-RAY DIFFRACTIONr_mcbond_other1.9642.61903
X-RAY DIFFRACTIONr_mcangle_it2.8693.9161130
X-RAY DIFFRACTIONr_mcangle_other2.8753.9151130
X-RAY DIFFRACTIONr_scbond_it3.1673.3291081
X-RAY DIFFRACTIONr_scbond_other3.1623.3341078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6864.7041497
X-RAY DIFFRACTIONr_long_range_B_refined6.67733.1312219
X-RAY DIFFRACTIONr_long_range_B_other6.67633.1532220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 57 -
Rwork0.251 1243 -
obs--99.69 %

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