5ERE | pdb_00005ere

Extracellular ligand binding receptor from Desulfohalobium retbaense DSM5692

• PDB DOI: https://doi.org/10.2210/pdb5ERE/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Desulfohalobium retbaense DSM 5692
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-14 Released: 2016-08-10 
• Deposition Author(s): Cuff, M., Wu, R., Endres, M., Pokkuluri, P.R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

A novel extracellular ligand receptor

Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 63.2 kDa 
• Atom Count: 4,328 
• Modeled Residue Count: 540 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A	568	Desulfohalobium retbaense DSM 5692	Mutation(s): 0  Gene Names: Dret_0059
UniProt
Find proteins for C8WZ86 (Desulfohalobium retbaense (strain ATCC 49708 / DSM 5692 / JCM 16813 / HR100)) Explore C8WZ86  Go to UniProtKB:  C8WZ86

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COI	B [auth A]	2-OXO-4-METHYLPENTANOIC ACID C6 H10 O3 BKAJNAXTPSGJCU-UHFFFAOYSA-N
CYT	C [auth A]	6-AMINOPYRIMIDIN-2(1H)-ONE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.946	α = 90
b = 104.946	β = 90
c = 140.181	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Cuff, M., Wu, R., Endres, M., Pokkuluri, P.R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary