Biological Assembly 1

Protein Symmetry: Cyclic - C3 (View in 3D)

Protein Stoichiometry: Homo 3-mer - A3

Macromolecule Content

• Unique protein chains: 1

4X31

Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation

• DOI: 10.2210/pdb4x31/pdb

• Classification: PROTON TRANSPORT
• Deposited: 2014-11-27 Released: 2015-02-18
• Deposition author(s): Nogly, P., James, D., Wang, D., White, T., Zatsepin, N., Shilova, A., Nelson, G., Liu, H., Johansson, L., Heymann, M., Jaeger, K., Metz, M., Wickstrand, C., Wu, W., Baath, P., Berntsen, P., Oberthuer, D., Panneels, V., Cherezov, V., Chapman, H., Spence, J., Schertler, G., Neutze, R., Moraes, I., Burghammer, M., Standfuss, J., Weierstall, U.
• Organism: Halobacterium salinarum

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.249
• R-Value Work: 0.205

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: PROTON TRANSPORT

Total Structure Weight: 28541.70

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Bacteriorhodopsin (BR)

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
LI1	A	1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]- 2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL LIPID FRAGMENT (Synonym) C42 H86 O3 YERVUJAKCNBGCR-BIHSMRAKSA-N	Poseview Image of LI1 in 4X31 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
RET	A	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N	Poseview Image of RET in 4X31 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.249
• R-Value Work: 0.205
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 62.79	α = 90.00
b = 62.79	β = 90.00
c = 109.67	γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2014-11-27
• Released Date: 2015-02-18
• Deposition author(s): Nogly, P., James, D., Wang, D., White, T., Zatsepin, N., Shilova, A., Nelson, G., Liu, H., Johansson, L., Heymann, M., Jaeger, K., Metz, M., Wickstrand, C., Wu, W., Baath, P., Berntsen, P., Oberthuer, D., Panneels, V., Cherezov, V., Chapman, H., Spence, J., Schertler, G., Neutze, R., Moraes, I., Burghammer, M., Standfuss, J., Weierstall, U.

Revision History

• 2015-03-11
  Type: Database references
• 2015-04-22
  Type: Database references