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- PDB-4xxj: Crystal Structure of Escherichia coli-Expressed Halobacterium sal... -

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Basic information

Entry
Database: PDB / ID: 4xxj
TitleCrystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form
ComponentsBacteriorhodopsin
KeywordsION TRANSPORT / PROTON PUMP
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
EICOSANE / Chem-MPG / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBratanov, D. / Balandin, T. / Round, E. / Gushchin, I. / Gordeliy, V.
CitationJournal: Plos One / Year: 2015
Title: An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin.
Authors: Bratanov, D. / Balandin, T. / Round, E. / Shevchenko, V. / Gushchin, I. / Polovinkin, V. / Borshchevskiy, V. / Gordeliy, V.
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
C: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,60439
Polymers88,2103
Non-polymers10,39436
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18470 Å2
ΔGint137 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.840, 60.760, 113.360
Angle α, β, γ (deg.)90.00, 99.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 29403.305 Da / Num. of mol.: 3 / Fragment: UNP residues 14-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945
#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: The crystals were grown using in meso crystallization technique

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→49.2 Å / Num. obs: 56113 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.102 / Mean I/σ(I) obs: 1.41 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.9→49.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.793 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 2770 5 %RANDOM
Rwork0.18345 ---
obs0.18502 52689 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20.01 Å2
2---1.03 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5279 0 320 90 5689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025727
X-RAY DIFFRACTIONr_bond_other_d0.0010.025983
X-RAY DIFFRACTIONr_angle_refined_deg0.9382.0187698
X-RAY DIFFRACTIONr_angle_other_deg1.3273.00313537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9495683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32322.364165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01715822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.981515
X-RAY DIFFRACTIONr_chiral_restr0.0540.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215948
X-RAY DIFFRACTIONr_gen_planes_other00.021220
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_it3.5283.2062726
X-RAY DIFFRACTIONr_mcbond_other3.5293.2052725
X-RAY DIFFRACTIONr_mcangle_it4.5544.7953402
X-RAY DIFFRACTIONr_mcangle_other4.5574.7953403
X-RAY DIFFRACTIONr_scbond_it4.5573.653001
X-RAY DIFFRACTIONr_scbond_other4.5563.653002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2355.2554294
X-RAY DIFFRACTIONr_long_range_B_refined7.7126.9746768
X-RAY DIFFRACTIONr_long_range_B_other7.7126.9786769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 202 -
Rwork0.341 3836 -
obs--98.15 %

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