4PAG | pdb_00004pag

ABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946

• PDB DOI: https://doi.org/10.2210/pdb4PAG/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Sulfurospirillum deleyianum DSM 6946
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-08 Released: 2014-04-30 
• Deposition Author(s): Chang, C., Endres, M., Li, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structure of ABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946

Chang, C., Endres, M., Li, H., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.73 kDa 
• Atom Count: 6,003 
• Modeled Residue Count: 645 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A, B	324	Sulfurospirillum deleyianum DSM 6946	Mutation(s): 0  Gene Names: Sdel_2069
UniProt
Find proteins for D1B4R1 (Sulfurospirillum deleyianum (strain ATCC 51133 / DSM 6946 / 5175)) Explore D1B4R1  Go to UniProtKB:  D1B4R1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], F [auth B], G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
HIS	E [auth A]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
PEG	D [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.055	α = 90
b = 50.813	β = 98
c = 91.544	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Chang, C., Endres, M., Li, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Source and taxonomy
• Version 1.2: 2017-03-22
  Changes: Source and taxonomy
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary