5ER3 | pdb_00005er3

Crystal structure of ABC transporter system solute-binding protein from Rhodopirellula baltica SH 1

• PDB DOI: https://doi.org/10.2210/pdb5ER3/pdb

• Classification: solute-binding protein
• Organism(s): Rhodopirellula baltica SH 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-13 Released: 2015-11-25 
• Deposition Author(s): Chang, C., Duke, N., Endres, M., Mack, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of ABC transporter system solute-binding protein from Rhodopirellula baltica SH 1

Chang, C., Duke, N., Endres, M., Mack, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.81 kDa 
• Atom Count: 2,453 
• Modeled Residue Count: 318 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, periplasmic sugar-binding protein	A	341	Rhodopirellula baltica SH 1	Mutation(s): 0  Gene Names: RB10898
UniProt
Find proteins for Q7UK26 (Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)) Explore Q7UK26  Go to UniProtKB:  Q7UK26

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [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: 2.10 Å
• R-Value Free:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.755	α = 90
b = 95.576	β = 90
c = 46.245	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Chang, C., Duke, N., Endres, M., Mack, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary