4JOQ

Putative ribose ABC transporter, periplasmic solute-binding protein from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb4JOQ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Cereibacter sphaeroides ATCC 17025
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-03-18 Released: 2013-04-10 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.142 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Literature

Putative ribose ABC transporter, periplasmic solute-binding protein from Rhodobacter sphaeroides.

Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.17 kDa 
• Atom Count: 4,906 
• Modelled Residue Count: 592 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC ribose transporter, periplasmic solute-binding protein	A, B	297	Cereibacter sphaeroides ATCC 17025	Mutation(s): 2  Gene Names: RbsB, Rsph17025_2685
UniProt
Find proteins for A4WW08 (Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)) Explore A4WW08  Go to UniProtKB:  A4WW08

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 0.142 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M34JOQ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.096	α = 90
b = 86.096	β = 90
c = 199.986	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary