2AT9

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution.

Mitsuoka, K.Hirai, T.Murata, K.Miyazawa, A.Kidera, A.Kimura, Y.Fujiyoshi, Y.

(1999) J Mol Biol 286: 861-882

  • DOI: https://doi.org/10.1006/jmbi.1998.2529
  • Primary Citation of Related Structures:  
    2AT9

  • PubMed Abstract: 

    Electron crystallography has the potential to visualise the charge status of atoms. This is due to the significantly different scattering factors of neutral and ionised atoms for electrons in the low-resolution range (typically less than 5 A). In previous work, we observed two different types of densities around acidic residues in the experimental (|Fo|) map of bacteriorhodopsin (bR), a light-driven proton pump. We suggested that these might reflect different states of the acidic residues; namely, the protonated (neutral) and the deprotonated (negatively charged) state. To evaluate the observed charge more quantitatively, we refined the atomic model for bR and eight surrounding lipids using our electron crystallographic data set between 8.0 and 3.0 A resolution, where the charge effect is small. The refined model yielded an R-factor of 23.7% and a free R-factor of 33.0%. To evaluate the effect of charges on the density map, we calculated a difference (|Fo|-|Fc|) map including data of a resolution lower than 8.0 A resolution, where the charge effect is significant. We found strong peaks in the difference map mainly in the backbone region of the transmembrane helices. We interpreted these peaks to come from the polarisation of the polar groups in the main chain of the alpha-helices and we examined this by assuming a partial charge of 0.5 for the peptide carbonyl groups. The resulting R and free R-factors dropped from 0.250 and 0.341 to 0.246 and 0.336, respectively. Furthermore, we also observed some strong peaks around some side-chains, which could be assigned to positively charged atoms. Thus, we could show that Asp36 and Asp102 are likely to interact with cations nearby. In addition, peaks found around the acidic residues Glu74, Glu194 and Glu212 have different features and might represent positive charges on polarised water molecules or hydroxonium ions.


  • Organizational Affiliation

    Department of Biophysics Faculty of Science, Kyoto University, Oiwake-cho Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan. kaorum@em.biophys.kyoto-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BACTERIORHODOPSIN248Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2DP
Query on 2DP

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL
C47 H98 O11 P2
ORVRQEXCVQTLMU-JCHKDBOHSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 62.45β = 90
c = 100γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTX-PLOR

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2024-06-05
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence
  • Version 2.1: 2024-10-23
    Changes: Structure summary