Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.54 kDa 
• Atom Count: 1848 
• Modelled Residue Count: 229 
• Deposited Residue Count: 229 
• Unique protein chains: 1

4X31

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

• PDB DOI: 10.2210/pdb4X31/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum NRC-1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.

Nogly, P., James, D., Wang, D., White, T.A., Zatsepin, N., Shilova, A., Nelson, G., Liu, H., Johansson, L., Heymann, M., Jaeger, K., Metz, M., Wickstrand, C., Wu, W., Bath, P., Berntsen, P., Oberthuer, D., Panneels, V., Cherezov, V., Chapman, H., Schertler, G., Neutze, R., Spence, J., Moraes, I., Burghammer, M., Standfuss, J., Weierstall, U.

(2015) IUCrJ 2: 168-176

• PubMed: 25866654 
• DOI: 10.1107/S2052252514026487
• Primary Citation of Related Structures:  
  4X31, 4X32


• PubMed Abstract: 
  

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.

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Organizational Affiliation: 

Department of Physics, Arizona State University, Tempe, AZ 85287, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	229	Halobacterium salinarum NRC-1	Mutation(s): 0  Gene Names: bop, VNG_1467G Membrane Entity: Yes
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945  Go to UniProtKB:  P02945

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LI1	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL C42 H86 O3 YERVUJAKCNBGCR-BIHSMRAKSA-N
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.79	α = 90
b = 62.79	β = 90
c = 109.67	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2015-04-22
  Changes: Database references