3HAN | pdb_00003han

Crystal structure of bacteriorhodopsin mutant V49A crystallized from bicelles

• PDB DOI: https://doi.org/10.2210/pdb3HAN/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Halobacterium salinarum
• Expression System: Halobacterium salinarum
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2009-05-02 Released: 2009-09-22 
• Deposition Author(s): Joh, N.H., Yang, D., Bowie, J.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.282 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Similar energetic contributions of packing in the core of membrane and water-soluble proteins.

Joh, N.H., Oberai, A., Yang, D., Whitelegge, J.P., Bowie, J.U.

(2009) J Am Chem Soc 131: 10846-10847

• PubMed: 19603754 
• DOI: https://doi.org/10.1021/ja904711k
• Primary Citation Related Structures: 
  3HAN, 3HAO, 3HAP, 3HAQ, 3HAR, 3HAS


• PubMed Abstract: 
  

  A major driving force for water-soluble protein folding is the hydrophobic effect, but membrane proteins cannot make use of this stabilizing contribution in the apolar core of the bilayer. It has been proposed that membrane proteins compensate by packing more efficiently. We therefore investigated packing contributions experimentally by observing the energetic and structural consequences of cavity creating mutations in the core of a membrane protein. We observed little difference in the packing energetics of water and membrane soluble proteins. Our results imply that other mechanisms are employed to stabilize the structure of membrane proteins.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.19 kDa 
• Atom Count: 1,771 
• Modeled Residue Count: 225 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	249	Halobacterium salinarum	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.282 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.948	α = 90
b = 102.878	β = 90
c = 128.422	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Joh, N.H., Yang, D., Bowie, J.U.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary