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- PDB-7q37: Crystal structure of proton pump MAR rhodopsin pressurized with k... -

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Basic information

Entry
Database: PDB / ID: 7q37
TitleCrystal structure of proton pump MAR rhodopsin pressurized with krypton
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump rhodopsin
Function / homology
Function and homology information


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
HEXANE / KRYPTON / EICOSANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesCandidatus Actinomarina minuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,56840
Polymers24,3051
Non-polymers6,26339
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint72 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.897, 40.381, 60.619
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-328-

KR

21A-330-

KR

31A-462-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / MAR rhodopsin


Mass: 24305.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: S5DM51

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Non-polymers , 5 types, 138 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.: 14 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 2.6 M ammonium sulfate, 0.1 M sodium acetate, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. obs: 22357 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rrim(I) all: 0.14 / Net I/σ(I): 7.74
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2971 / CC1/2: 0.491 / Rrim(I) all: 1.299 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSI

5jsi


Resolution: 2.25→59.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.704 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24468 570 4.9 %RANDOM
Rwork0.17785 ---
obs0.18117 11102 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-1.12 Å2
2---1.57 Å20 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 2.25→59.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 201 99 1976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131887
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171967
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6512495
X-RAY DIFFRACTIONr_angle_other_deg1.2881.5534508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92619.88688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7381510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it2.553.234869
X-RAY DIFFRACTIONr_mcbond_other2.523.227868
X-RAY DIFFRACTIONr_mcangle_it3.5994.8431084
X-RAY DIFFRACTIONr_mcangle_other3.6044.8491085
X-RAY DIFFRACTIONr_scbond_it3.5274.0131017
X-RAY DIFFRACTIONr_scbond_other3.5254.0151018
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.335.671411
X-RAY DIFFRACTIONr_long_range_B_refined7.11440.7552223
X-RAY DIFFRACTIONr_long_range_B_other6.98940.4132201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 37 -
Rwork0.262 787 -
obs--98.92 %

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