6GUZ

Ground state structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature

• PDB DOI: https://doi.org/10.2210/pdb6GUZ/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halorubrum sodomense
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-06-19 Released: 2019-10-09 
• Deposition Author(s): Moraes, I., Judge, P.J., Bada Juarez, J.F., Vinals, J., Axford, D., Watts, A.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Room temperature structure of the Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich

Bada Juarez, J.F., Judge, P.J., Vinals, J., Axford, D., Birch, J., Aller, P., Butryn, A., Owen, R.L., Sherrell, D.A., Beale, J.H., Orville, A.M., Watts, A., Moraes, I.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 27.85 kDa 
• Atom Count: 2,050 
• Modelled Residue Count: 240 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaerhodopsin-3	A	241	Halorubrum sodomense	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P96787 (Halorubrum sodomense) Explore P96787  Go to UniProtKB:  P96787

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
R16	C [auth A], E [auth A]	HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N
D10	J [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9	D [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	nonane C9 H20 BKIMMITUMNQMOS-UHFFFAOYSA-N
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.254	α = 90
b = 48.302	β = 90
c = 104.835	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Moraes, I., Judge, P.J., Bada Juarez, J.F., Vinals, J., Axford, D., Watts, A.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202892/Z/16/Z
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N006011/1

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 2.0: 2020-03-11
  Changes: Polymer sequence
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description